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amber.py
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amber.py
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#!/usr/bin/python
# -*- coding: utf-8 -*-
import os, sys, string, shutil
import subprocess as commands
AMBERHOME = "/home/helix/amber16/"
AMBEREXEC = "bin/pmemd.cuda"
os.environ['AMBERHOME'] = "/home/helix/amber16/"
os.environ['CUDA_HOME'] = "/usr/local/cuda-8.0/"
os.environ['PATH'] = "/usr/local/cuda-8.0/bin:$PATH"
os.environ['LD_LIBRARY_PATH'] = "/usr/local/cuda-8.0/lib64/:$LD_LIBRARY_PATH"
os.environ['LD_LIBRARY_PATH'] = "/home/helix/amber16/lib/:$LD_LIBRARY_PATH"
dict_lipid = {}
dict_lipid["HGA"] = "AMT C07"
dict_lipid["HGB"] = "BMT C07"
dict_lipid["OGA"] = "AMT C08"
dict_lipid["OGB"] = "BMT C08"
dict_lipid["NGA"] = "AMT C09"
dict_lipid["NGB"] = "BMT C09"
dict_lipid["DGA"] = "AMT C10"
dict_lipid["DGB"] = "BMT C10"
dict_lipid["UGA"] = "AMT C11"
dict_lipid["UGB"] = "BMT C11"
dict_lipid["EGA"] = "AMT C12"
dict_lipid["EGB"] = "BMT C12"
dict_lipid["HMA"] = "AMT AMG C07"
dict_lipid["HMB"] = "AMT BMG C07"
dict_lipid["OMA"] = "AMT AMG C08"
dict_lipid["OMB"] = "AMT BMG C08"
dict_lipid["NMA"] = "AMT AMG C09"
dict_lipid["NMB"] = "AMT BMG C09"
dict_lipid["DMA"] = "AMT AMG C10"
dict_lipid["DMB"] = "AMT BMG C10"
dict_lipid["UMA"] = "AMT AMG C11"
dict_lipid["UMB"] = "AMT BMG C11"
dict_lipid["EMA"] = "AMT AMG C12"
dict_lipid["EMB"] = "AMT BMG C12"
dict_lipid["SDS"] = "SDS"
dict_lipid["UGN"] = "UGN"
dict_lipid["UGV"] = "UGV"
dict_lipid["UGL"] = "UGL"
dict_lipid["UAG"] = "UAG"
dict_lipid["UAA"] = "UAA"
dict_lipid["UAV"] = "UAV"
dict_lipid["UAL"] = "UAL"
dict_lipid["UVG"] = "UVG"
dict_lipid["UVA"] = "UVA"
dict_lipid["UVV"] = "UVV"
dict_lipid["UVL"] = "UVL"
dict_lipid["ULG"] = "ULG"
dict_lipid["ULA"] = "ULA"
dict_lipid["ULV"] = "ULV"
dict_lipid["ULL"] = "ULL"
dict_lipid["SUA"] = "SUA"
dict_lipid["SUV"] = "SUV"
dict_lipid["SUL"] = "SUL"
aAAS = ['UGN','UGV','UGL','UAG','UAA','UAV','UAL','UVG','UVA','UVV','UVL','ULG','ULA','ULV','ULL','SUA','SUV','SUL']
class do_amber():
def __init__(self,sType,sMName,sIonP,sIonN,sConc,sBoxDim,iNo,sGPU_ID):
self.sType = sType
self.sMName = sMName
self.sIonP = sIonP
self.sIonN = sIonN
self.sConc = sConc
self.sBoxDim = sBoxDim
self.iNo = iNo
self.sGPU_ID = sGPU_ID
def calc_ions(self,sBoxSize,sConc):
# (0.5 Mol) * (6.02*10^23) / 1dm^3 / ((10^9)^3 * (Ang^3/dm^3)) -> 3*E-4 molecules/Ang^3 -> box = 77760 Ang^3 -> 23.328 molecules
fMolAng = float(sConc) * (6.02*10**23) / ((10**9)**3) # molecules/Ang^3
sNoIons = str(int(round(fMolAng * float(sBoxSize),0)))
return sNoIons,sNoIons
def check_quality(self):
iC = int(commands.getstatusoutput("/usr/bin/grep NaN equil*.out | /usr/bin/wc -l")[1])
iD = int(commands.getstatusoutput("/usr/bin/grep ERROR *.log | /usr/bin/wc -l")[1])
iS = iC + iD
if(iS > 0):
print(" Error during equilibration. Restart.\n")
return False
else:
return True
def runLeap(self):
commands.getstatusoutput(AMBERHOME+"bin/tleap -f leap_"+self.sMName+".ff14SB")
def genLeapFile(self):
fXB = float(self.sBoxDim.split()[0])
fYB = float(self.sBoxDim.split()[1])
fZB = float(self.sBoxDim.split()[2])
sBoxSize = str(fXB*fYB*fZB)
sNoP,sNoN = self.calc_ions(sBoxSize,self.sConc)
sPNam = self.sIonP
if(self.sIonP == 'Mg2+' or self.sIonP == 'Ca2+'):
sNoN = str(2*int(sNoN))
self.sIonP = self.sIonP[:2].upper()
print( " Add "+sNoP+" "+sPNam+" salt ions")
print( " Add "+sNoN+" "+self.sIonN+" salt ions\n")
if(self.sType == "SDS" or self.sType in aAAS):
if(self.sIonP == 'MG' or self.sIonP == 'CA'):
sNoP = str( int(sNoP) + int(round(float(self.iNo)/2.0,0)) )
print( " Add "+str( int(round(float(self.iNo)/2.0,0)) )+" "+sPNam+" ions to neutralize the system\n")
else:
sNoP = str( int(sNoP)+int(self.iNo) )
print( " Add "+str(self.iNo)+" "+sPNam+" ions to neutralize the system\n")
sContent = """
logFile leap.log
#
# ----- leaprc for loading the ff14SB force field
# ----- NOTE: this is designed for PDB format 3!
# Uses frcmod.ff14SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
#
# load atom type hybridizations
#
addAtomTypes {
{ "H" "H" "sp3" }
{ "HO" "H" "sp3" }
{ "HS" "H" "sp3" }
{ "H1" "H" "sp3" }
{ "H2" "H" "sp3" }
{ "H3" "H" "sp3" }
{ "H4" "H" "sp3" }
{ "H5" "H" "sp3" }
{ "HW" "H" "sp3" }
{ "HC" "H" "sp3" }
{ "HA" "H" "sp3" }
{ "HP" "H" "sp3" }
{ "HZ" "H" "sp3" }
{ "OH" "O" "sp3" }
{ "OS" "O" "sp3" }
{ "O" "O" "sp2" }
{ "O2" "O" "sp2" }
{ "OP" "O" "sp2" }
{ "OW" "O" "sp3" }
{ "CT" "C" "sp3" }
{ "CX" "C" "sp3" }
{ "C8" "C" "sp3" }
{ "2C" "C" "sp3" }
{ "3C" "C" "sp3" }
{ "CH" "C" "sp3" }
{ "CS" "C" "sp2" }
{ "C" "C" "sp2" }
{ "CO" "C" "sp2" }
{ "C*" "C" "sp2" }
{ "CA" "C" "sp2" }
{ "CB" "C" "sp2" }
{ "CC" "C" "sp2" }
{ "CN" "C" "sp2" }
{ "CM" "C" "sp2" }
{ "CK" "C" "sp2" }
{ "CQ" "C" "sp2" }
{ "CD" "C" "sp2" }
{ "C5" "C" "sp2" }
{ "C4" "C" "sp2" }
{ "CP" "C" "sp2" }
{ "CI" "C" "sp3" }
{ "CJ" "C" "sp2" }
{ "CW" "C" "sp2" }
{ "CV" "C" "sp2" }
{ "CR" "C" "sp2" }
{ "CA" "C" "sp2" }
{ "CY" "C" "sp2" }
{ "C0" "Ca" "sp3" }
{ "N" "N" "sp2" }
{ "NA" "N" "sp2" }
{ "N2" "N" "sp2" }
{ "N*" "N" "sp2" }
{ "NP" "N" "sp2" }
{ "NQ" "N" "sp2" }
{ "NB" "N" "sp2" }
{ "NC" "N" "sp2" }
{ "NT" "N" "sp3" }
{ "NY" "N" "sp2" }
{ "N3" "N" "sp3" }
{ "S" "S" "sp3" }
{ "SH" "S" "sp3" }
{ "P" "P" "sp3" }
{ "LP" "" "sp3" }
{ "F" "F" "sp3" }
{ "Cl" "Cl" "sp3" }
{ "Br" "Br" "sp3" }
{ "I" "I" "sp3" }
{ "F-" "F" "sp3" }
{ "Cl-" "Cl" "sp3" }
{ "Br-" "Br" "sp3" }
{ "I-" "I" "sp3" }
{ "Li+" "Li" "sp3" }
{ "Na+" "Na" "sp3" }
{ "K+" "K" "sp3" }
{ "Mg2+" "Mg" "sp3" }
{ "Zn2+" "Zn" "sp3" }
{ "Ca2+" "Ca" "sp3" }
# glycam
# { "OG" "O" "sp3" }
# { "OL" "O" "sp3" }
# { "AC" "C" "sp3" }
# { "EC" "C" "sp3" }
# { "DA" "Ca" "sp3" }
# { "DB" "Ca" "sp3" }
# { "DC" "Ca" "sp3" }
# { "DD" "Ca" "sp3" }
# { "DE" "Ca" "sp3" }
# { "DF" "Ca" "sp3" }
# { "Ca" "Ca" "sp3" }
}
#
# Load the main parameter set.
#
parm10 = loadamberparams parm10.dat
frcmod14SB = loadamberparams frcmod.ff14SB
#
# Load main chain and terminating amino acid libraries, nucleic acids
#
loadOff amino12.lib
loadOff aminoct12.lib
loadOff aminont12.lib
#
# Load water and ions
#
loadOff atomic_ions.lib
loadOff solvents.lib
HOH = TP3
WAT = TP3
loadamberparams frcmod.ions1lm_126_tip3p
loadamberparams frcmod.ions234lm_126_tip3p
#
# Define the PDB name map for the amino acids and nucleic acids
#
addPdbResMap {
{ 0 "HYP" "NHYP" } { 1 "HYP" "CHYP" }
{ 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
{ 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
{ 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
{ 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
{ 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
{ 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
{ 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
{ 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
{ 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
{ 0 "HID" "NHID" } { 1 "HID" "CHID" }
{ 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
{ 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
{ 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
{ 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
{ 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
{ 0 "MET" "NMET" } { 1 "MET" "CMET" }
{ 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
{ 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
{ 0 "SER" "NSER" } { 1 "SER" "CSER" }
{ 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
{ 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
{ 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
{ 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
{ 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
}
# try to be good about reading in really old atom names as well:
addPdbAtomMap {
{ "O5*" "O5'" }
{ "C5*" "C5'" }
{ "C4*" "C4'" }
{ "O4*" "O4'" }
{ "C3*" "C3'" }
{ "O3*" "O3'" }
{ "C2*" "C2'" }
{ "O2*" "O2'" }
{ "C1*" "C1'" }
{ "C5M" "C7" }
{ "H1*" "H1'" }
{ "H2*1" "H2'" }
{ "H2*2" "H2''" }
{ "H2'1" "H2'" }
{ "H2'2" "H2''" }
{ "H3*" "H3'" }
{ "H4*" "H4'" }
{ "H5*1" "H5'" }
{ "H5*2" "H5''" }
{ "H5'1" "H5'" }
{ "H5'2" "H5''" }
{ "HO'2" "HO2'" }
{ "H5T" "HO5'" }
{ "H3T" "HO3'" }
{ "O1'" "O4'" }
{ "OA" "OP1" }
{ "OB" "OP2" }
{ "O1P" "OP1" }
{ "O2P" "OP2" }
}
#
# assume that most often proteins use HIE
#
#NHIS = NHIE
#HIS = HIE
#CHIS = CHIE
#
# My stuff
#
#
# Bondi radii for igb = 5
#
set default PBradii mbondi2
loadamberparams GLYCAM_06j.dat
"""
sContent2 = ""
aOff = dict_lipid[self.sType].split()
for i in range(len(aOff)):
sContent2 += "loadOff ../amber/glycam_lib/"+aOff[i]+".off\n"
sTag = aOff[len(aOff)-1]
if(aOff[0] in aAAS):
sContent2 += "source leaprc.gaff2\n"
sContent2 += "loadamberparams gaff2.dat\n"
sContent2 += "loadamberparams ../amber/glycam_lib/"+aOff[0]+".frcmod\n"
sContent2 += "PDB = loadpdb "+self.sMName+".pdb\n"
if(aOff[0] in aAAS):
iZC = 1
for k in range(self.iNo):
sContent2 += "bond PDB."+str(iZC)+".C11 PDB."+str(iZC+1)+".N\n"
iZC +=3
commands.getstatusoutput("/bin/sed -i \'s/CLI/"+aOff[0]+"/g\' "+self.sMName+".pdb")
sNoP = str(0)
sNoN = str(0)
if(aOff[0] in ["UVV","ULL","UAA"]):
ff2 = open("tmpf.pdb","w")
ff = open(self.sMName+".pdb","r")
aRes = []
iZ = 1
iCo = 0
for line in ff.readlines():
if(line[:4] == "ATOM"):
sAA = line[16:20]
aRes.append(sAA)
if(len(aRes) > 1):
if(aRes[iCo] != aRes[iCo-1]):
iZ +=1
iCo+=1
ff2.write(line[:16]+" "+line[17:25]+str(iZ)+line[27:])
else:
ff2.write(line)
ff.close()
ff2.close()
shutil.copy("tmpf.pdb",self.sMName+".pdb")
commands.getstatusoutput("/bin/sed -i 's/CLI/"+sTag+"/g' "+self.sMName+".pdb")
sContent2 += "set PDB box {"+self.sBoxDim+"}\n"
sContent2 += "solvatebox PDB TIP3PBOX 0.0\n"
# sContent2 += "solvateoct PDB TIP3PBOX 11.0\n"
sContent2 += "addions PDB "+self.sIonP+" "+sNoP+"\n"
sContent2 += "addions PDB "+self.sIonN+" "+sNoN+"\n"
sContent2 += "savepdb PDB "+self.sMName+"_solv_ions.pdb\n"
sContent2 += "saveamberparm PDB "+self.sMName+"_solv_ions.prmtop "+self.sMName+"_solv_ions.inpcrd\n"
sContent2 += "quit\n"
FLeap = open("leap_"+self.sMName+".ff14SB","w")
FLeap.write(sContent)
FLeap.write(sContent2)
FLeap.close()
return self.sType
def minimize(self,iMaxcyc):
sCon = ""
aOff = dict_lipid[self.sType].split()
iOff = len(aOff)
if(iOff < 3):
sCon = "* * * "+aOff[0]+"\n* * * C12"
else:
sCon = "* * * "+aOff[0]+"\n* * * "+aOff[1]+"\n* * * C12"
if(iOff == 1):
if(aOff[0] == "UGN"):
sCon = "* * * GLY\n* * * ALA\n* * * C10"
if(aOff[0] == "UGV"):
sCon = "* * * GLY\n* * * VAL\n* * * C10"
if(aOff[0] == "UGL"):
sCon = "* * * GLY\n* * * LEU\n* * * C10"
if(aOff[0] == "UAG"):
sCon = "* * * ALA\n* * * GLY\n* * * C10"
if(aOff[0] == "UAA"):
sCon = "* * * ALA\n* * * ALA\n* * * C10"
if(aOff[0] == "UAV"):
sCon = "* * * ALA\n* * * VAL\n* * * C10"
if(aOff[0] == "UAL"):
sCon = "* * * ALA\n* * * LEU\n* * * C10"
if(aOff[0] == "UVG"):
sCon = "* * * VAL\n* * * GLY\n* * * C10"
if(aOff[0] == "UVA"):
sCon = "* * * VAL\n* * * ALA\n* * * C10"
if(aOff[0] == "UVV"):
sCon = "* * * VAL\n* * * VAL\n* * * C10"
if(aOff[0] == "UVL"):
sCon = "* * * VAL\n* * * LEU\n* * * C10"
if(aOff[0] == "ULG"):
sCon = "* * * LEU\n* * * GLY\n* * * C10"
if(aOff[0] == "ULA"):
sCon = "* * * LEU\n* * * ALA\n* * * C10"
if(aOff[0] == "ULV"):
sCon = "* * * LEU\n* * * VAL\n* * * C10"
if(aOff[0] == "ULL"):
sCon = "* * * LEU\n* * * LEU\n* * * C10"
if(aOff[0] == "SUA"):
sCon = "* * * ALA\n* * * C10"
if(aOff[0] == "SUV"):
sCon = "* * * VAL\n* * * C10"
if(aOff[0] == "SUL"):
sCon = "* * * LEU\n* * * C10"
sInput = """Initial repair minimization without position restraints
&cntrl
nmropt = 0,
ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
ntpr = 100, ntwx = 0, ntwv = 0, ntwe = 0,
ioutfm = 0, ntwprt = 0,
ntf = 1, ntb = 1, dielc = 1, igb = 0,
cut = 8.0, nsnb = 25,
ipol = 0,
ibelly = 0, ntr = 0,
imin = 1,
maxcyc = """+str(iMaxcyc)+""",
ncyc = 100000,
ntmin = 1, dx0 = 0.1, drms = 0.0001,
nstlim = 10000,
nscm = 0,
t = 0.0, dt = 0.002,
temp0 = 300.0, tempi = 300.0,
ig = 71277,
ntt = 0,
tautp = 0.5,
ntp = 0, pres0 = 1.0, comp = 44.6,
taup = 5.0,
ntc = 1, tol = 0.000001
&end
END
"""
sFile = "min1_"+self.sMName
FMin = open(sFile+".in","w")
FMin.write(sInput)
FMin.close()
os.environ['CUDA_VISIBLE_DEVICES'] = self.sGPU_ID
# commands.getstatusoutput(AMBERHOME+AMBEREXEC+" -O -i "+sFile+".in -o "+sFile+".out -p "+self.sMName+"_solv_ions.prmtop -c "+self.sMName+"_solv_ions.inpcrd -r "+sFile+".restrt -ref "+self.sMName+"_solv_ions.inpcrd")
os.system(AMBERHOME+AMBEREXEC+" -O -i "+sFile+".in -o "+sFile+".out -p "+self.sMName+"_solv_ions.prmtop -c "+self.sMName+"_solv_ions.inpcrd -r "+sFile+".restrt -ref "+self.sMName+"_solv_ions.inpcrd")
commands.getstatusoutput(AMBERHOME+"/bin/ambpdb -ctr -p "+self.sMName+"_solv_ions.prmtop < "+sFile+".restrt > "+sFile+".pdb")
sInput = """Water minimization with position restraints
&cntrl
nmropt = 0,
ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
ntpr = 100, ntwx = 0, ntwv = 0, ntwe = 0,
ioutfm = 0, ntwprt = 0,
ntf = 1, ntb = 1, dielc = 1, igb = 0,
cut = 8.0, nsnb = 25,
ipol = 0,
ibelly = 0, ntr = 1,
imin = 1,
maxcyc = 5000,
ncyc = 2000,
ntmin = 1, dx0 = 0.1, drms = 0.0001,
nstlim = 10000,
nscm = 0,
t = 0.0, dt = 0.002,
temp0 = 300.0, tempi = 300.0,
ig = 71277,
ntt = 0,
tautp = 0.5,
ntp = 0, pres0 = 1.0, comp = 44.6,
taup = 5.0,
ntc = 1, tol = 0.000001
&end
posres
25.0
FIND
"""+sCon+"""
SEARCH
RES 1 10000
END
END
"""
sFile = "min2_"+self.sMName
FMin = open(sFile+".in","w")
FMin.write(sInput)
FMin.close()
os.environ['CUDA_VISIBLE_DEVICES'] = self.sGPU_ID
commands.getstatusoutput(AMBERHOME+AMBEREXEC+" -O -i "+sFile+".in -o "+sFile+".out -p "+self.sMName+"_solv_ions.prmtop -c min1_"+self.sMName+".restrt -r "+sFile+".restrt -ref min1_"+self.sMName+".restrt")
commands.getstatusoutput(AMBERHOME+"/bin/ambpdb -ctr -p "+self.sMName+"_solv_ions.prmtop < "+sFile+".restrt > "+sFile+".pdb")
sInput = """Water minimization with position restraints
&cntrl
nmropt = 0,
ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
ntpr = 100, ntwx = 0, ntwv = 0, ntwe = 0,
ioutfm = 0, ntwprt = 0,
ntf = 1, ntb = 1, dielc = 1, igb = 0,
cut = 8.0, nsnb = 25,
ipol = 0,
ibelly = 0, ntr = 1,
imin = 1,
maxcyc = 5000,
ncyc = 2000,
ntmin = 1, dx0 = 0.1, drms = 0.0001,
nstlim = 10000,
nscm = 0,
t = 0.0, dt = 0.002,
temp0 = 300.0, tempi = 300.0,
ig = 71277,
ntt = 0,
tautp = 0.5,
ntp = 0, pres0 = 1.0, comp = 44.6,
taup = 5.0,
ntc = 1, tol = 0.000001
&end
posres
5.0
FIND
"""+sCon+"""
SEARCH
RES 1 10000
END
END
"""
sFile = "min3_"+self.sMName
FMin = open(sFile+".in","w")
FMin.write(sInput)
FMin.close()
os.environ['CUDA_VISIBLE_DEVICES'] = self.sGPU_ID
commands.getstatusoutput(AMBERHOME+AMBEREXEC+" -O -i "+sFile+".in -o "+sFile+".out -p "+self.sMName+"_solv_ions.prmtop -c min2_"+self.sMName+".restrt -r "+sFile+".restrt -ref min2_"+self.sMName+".restrt")
commands.getstatusoutput(AMBERHOME+"/bin/ambpdb -ctr -p "+self.sMName+"_solv_ions.prmtop < "+sFile+".restrt > "+sFile+".pdb")
return self
def equilibration(self):
sCon = ""
aOff = dict_lipid[self.sType].split()
iOff = len(aOff)
if(iOff < 3 and iOff > 1):
sCon = "C1 * * "+aOff[0]+"\nC12 * * C12"
if(iOff == 3):
sCon = "C1 * * "+aOff[0]+"\nC1 * * "+aOff[1]+"\nC12 * * C12"
if(iOff == 1):
sCon = "C1 * * "+aOff[0]+"\nC12 * * SDS"
if(iOff == 1):
if(aOff[0] in aAAS):
sCon = "C1 * * "+aOff[0]+"\nC10 * * "+aOff[0]
sInput ="""Minimization with position restraints
&cntrl
nmropt = 1,
ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
ntpr = 100, ntwx = 0, ntwv = 0, ntwe = 0,
ioutfm = 0, ntwprt = 0,
ntf = 1, ntb = 1, dielc = 1, igb = 0,
cut = 8.0, nsnb = 25,
ipol = 0,
ibelly = 0, ntr = 1,
imin = 1,
maxcyc = 5000,
ncyc = 200,
ntmin = 1, dx0 = 0.1, drms = 0.0001,
nstlim = 10000,
nscm = 0,
t = 0.0, dt = 0.002,
temp0 = 300.0, tempi = 300.0,
ig = 71277,
ntt = 0,
tautp = 0.5,
ntp = 0, pres0 = 1.0, comp = 44.6,
taup = 5.0,
ntc = 1, tol = 0.000001,
watnam='WAT', ! Water residues are named WAT
owtnm='O', ! Water oxygens are named O
&end
&wt
type='END'
&end
Membrane posres
5.0
FIND
"""+sCon+"""
SEARCH
RES 1 10000
END
END
DISANG=restraints01.rest
LISTIN=POUT
LISTOUT=POUT
"""
sFile = "equil0_"+self.sMName
FEQ = open(sFile+".in","w")
FEQ.write(sInput)
FEQ.close()
sInput ="""NVT MD with position restraints
&cntrl
nmropt = 1,
ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
ntpr = 5000, ntwx = 5000, ntwv = 0, ntwe = 0,
ioutfm = 0, ntwprt = 0,
ntf = 2, ntb = 1, dielc = 1, igb = 0,
cut = 8.0, nsnb = 25,
ipol = 0,
ibelly = 0, ntr = 1,
imin = 0,
maxcyc = 5000,
ncyc = 200,
ntmin = 1, dx0 = 0.1, drms = 0.0001,
nstlim = 25000,
nscm = 0,
t = 0.0, dt = 0.002,
temp0 = 300.0, tempi = 100.0,
ig = 71277,
ntt = 1,
tautp = 0.5,
ntp = 0, pres0 = 1.0, comp = 44.6,
taup = 5.0,
ntc = 2, tol = 0.000001,
watnam='WAT', ! Water residues are named WAT
owtnm='O', ! Water oxygens are named O
&end
&wt
type = 'TEMP0', istep1 = 0, istep2 = 20000,
value1 = 100.0, value2 = 300.0,
&end
&wt
type = 'TEMP0', istep1 = 20001, istep2 = 25000,
value1 = 300.0, value2 = 300.0,
&end
&wt
type = 'END'
&end
Membrane posres
25.0
FIND
"""+sCon+"""
SEARCH
RES 1 10000
END
END
DISANG=restraints01.rest
LISTIN=POUT
LISTOUT=POUT"""
sFile = "equil1_"+self.sMName
FEQ = open(sFile+".in","w")
FEQ.write(sInput)
FEQ.close()
sInput="""NPT MD with position restraints
&cntrl
nmropt = 1,
ntx = 7, irest = 1, ntrx = 1, ntxo = 1,
ntpr = 5000, ntwx = 5000, ntwv = 0, ntwe = 0,
ioutfm = 0, ntwprt = 0,
ntf = 2, ntb = 2, dielc = 1, igb = 0,
cut = 8.0, nsnb = 10,
ipol = 0,
ibelly = 0, ntr = 1,
imin = 0,
maxcyc = 5000,
ncyc = 200,
ntmin = 1, dx0 = 0.1, drms = 0.0001,
nstlim = 25000,
nscm = 0,
t = 50.0, dt = 0.002,
temp0 = 300.0, tempi = 300.0,
ig = 71277,
ntt = 1,
tautp = 0.5,
barostat = 1,
ntp = 1, pres0 = 1.0, comp = 44.6,
taup = 5.0,
ntc = 2, tol = 0.000001,
watnam='WAT', ! Water residues are named WAT
owtnm='O', ! Water oxygens are named O
&end
&wt
type='END'
&end
Membrane posres
25.0
FIND
"""+sCon+"""
SEARCH
RES 1 10000
END
END
DISANG=restraints01.rest
LISTIN=POUT
LISTOUT=POUT"""
for i in range(3):
sFile = "equil"+str(i+2)+"_"+self.sMName
FEQ = open(sFile+".in","w")
FEQ.write(sInput)
FEQ.close()
iN = 24.0
for i in range(12):
sFile = "equil"+str(i+5)+"_"+self.sMName
FEQ = open(sFile+".in","w")
iN -= 2.0
if(i <= 2):
sRest = "restraints02.rest"
if(i > 2):
sRest = "restraints03.rest"
if(i > 6):
sRest = "restraints04.rest"
if(i > 9):
sRest = "restraints05.rest"
sInput = """NVT MD with position restraints
&cntrl
nmropt = 1,
ntx = 7, irest = 1, ntrx = 1, ntxo = 1,
ntpr = 5000, ntwx = 5000, ntwv = 0, ntwe = 0,
ioutfm = 0, ntwprt = 0,
ntf = 2, ntb = 1, dielc = 1, igb = 0,
cut = 8.0, nsnb = 10,
ipol = 0,
ibelly = 0, ntr = 1,
imin = 0,
maxcyc = 5000,
ncyc = 100,
ntmin = 1, dx0 = 0.1, drms = 0.0001,
nstlim = 50000,
nscm = 0,
t = 100.0, dt = 0.002,
temp0 = 300.0, tempi = 300.0,
ig = 71277,
ntt = 1,
tautp = 0.5,
ntp = 0, pres0 = 1.0, comp = 44.6,
taup = 5.0,
ntc = 2, tol = 0.000001,
watnam='WAT', ! Water residues are named WAT
owtnm='O', ! Water oxygens are named O
jfastw = 0,
ivcap = 0, fcap = 1.5,
&end
&wt
type='END'
&end
Membrane posres
"""+str(iN)+"""
FIND
"""+sCon+"""
SEARCH
RES 1 10000
END
END
DISANG="""+sRest+"""
LISTIN=POUT
LISTOUT=POUT"""
FEQ.write(sInput)
FEQ.close()
sInput = """NVT MD without position restraints
&cntrl
nmropt = 0,
ntx = 7, irest = 1, ntrx = 1, ntxo = 1,
ntpr = 5000, ntwx = 5000, ntwv = 0, ntwe = 0,
ioutfm = 0, ntwprt = 0,
ntf = 2, ntb = 1, dielc = 1, igb = 0,
cut = 8.0, nsnb = 10,
ipol = 0,
ibelly = 0, ntr = 0,
imin = 0,
maxcyc = 5000,
ncyc = 200,
ntmin = 1, dx0 = 0.1, drms = 0.0001,
nstlim = 50000,
nscm = 0,
t = 200.0, dt = 0.002,
temp0 = 300.0, tempi = 300.0,
ig = 71277,
ntt = 1,
tautp = 0.5,
ntp = 0, pres0 = 1.0, comp = 44.6,
taup = 5.0,
ntc = 2, tol = 0.000001,
watnam='WAT', ! Water residues are named WAT
owtnm='O', ! Water oxygens are named O
&end
END"""
sFile = "equil17_"+self.sMName
FEQ = open(sFile+".in","w")
FEQ.write(sInput)
FEQ.close()
FEptraj = open(self.sMName+"_ptraj.in","w")
FElog = open(self.sMName+"_equil.log","a")
print(" Equilibration in progress... 10%")
os.environ['CUDA_VISIBLE_DEVICES'] = self.sGPU_ID
FElog.write(commands.getstatusoutput(AMBERHOME+AMBEREXEC+" -O -i equil0_"+self.sMName+".in -o equil0_"+self.sMName+".out -p "+self.sMName+"_solv_ions.prmtop -c min3_"+self.sMName+".restrt -r equil0_"+self.sMName+".restrt -ref "+self.sMName+"_solv_ions.inpcrd")[1]+"\n")
commands.getstatusoutput(AMBERHOME+"/bin/ambpdb -ctr -p "+self.sMName+"_solv_ions.prmtop < equil0_"+self.sMName+".restrt > equil0_"+self.sMName+".pdb")
if(self.check_quality() == False):
return False
print(" Equilibration in progress... 15%")
os.environ['CUDA_VISIBLE_DEVICES'] = self.sGPU_ID
FElog.write(commands.getstatusoutput(AMBERHOME+AMBEREXEC+" -O -i equil1_"+self.sMName+".in -o equil1_"+self.sMName+".out -p "+self.sMName+"_solv_ions.prmtop -c equil0_"+self.sMName+".restrt -r equil1_"+self.sMName+".restrt -ref equil0_"+self.sMName+".restrt -x equil1_"+self.sMName+".mdcrd")[1]+"\n")
FEptraj.write("trajin equil1_"+self.sMName+".mdcrd 1 100 1\n")
if(self.check_quality() == False):
return False
print(" Equilibration in progress... 20%")
os.environ['CUDA_VISIBLE_DEVICES'] = self.sGPU_ID
FElog.write(commands.getstatusoutput(AMBERHOME+AMBEREXEC+" -O -i equil2_"+self.sMName+".in -o equil2_"+self.sMName+".out -p "+self.sMName+"_solv_ions.prmtop -c equil1_"+self.sMName+".restrt -r equil2_"+self.sMName+".restrt -ref equil1_"+self.sMName+".restrt -x equil2_"+self.sMName+".mdcrd")[1]+"\n")
FEptraj.write("trajin equil2_"+self.sMName+".mdcrd 1 100 1\n")
if(self.check_quality() == False):
return False
print(" Equilibration in progress... 25%")
os.environ['CUDA_VISIBLE_DEVICES'] = self.sGPU_ID
FElog.write(commands.getstatusoutput(AMBERHOME+AMBEREXEC+" -O -i equil3_"+self.sMName+".in -o equil3_"+self.sMName+".out -p "+self.sMName+"_solv_ions.prmtop -c equil2_"+self.sMName+".restrt -r equil3_"+self.sMName+".restrt -ref equil2_"+self.sMName+".restrt -x equil3_"+self.sMName+".mdcrd")[1]+"\n")
FEptraj.write("trajin equil3_"+self.sMName+".mdcrd 1 100 1\n")
if(self.check_quality() == False):
return False
print(" Equilibration in progress... 30%")
os.environ['CUDA_VISIBLE_DEVICES'] = self.sGPU_ID
FElog.write(commands.getstatusoutput(AMBERHOME+AMBEREXEC+" -O -i equil4_"+self.sMName+".in -o equil4_"+self.sMName+".out -p "+self.sMName+"_solv_ions.prmtop -c equil3_"+self.sMName+".restrt -r equil4_"+self.sMName+".restrt -ref equil3_"+self.sMName+".restrt -x equil4_"+self.sMName+".mdcrd")[1]+"\n")
FEptraj.write("trajin equil4_"+self.sMName+".mdcrd 1 100 1\n")
if(self.check_quality() == False):
return False
print(" Equilibration in progress... 35%")
os.environ['CUDA_VISIBLE_DEVICES'] = self.sGPU_ID
FElog.write(commands.getstatusoutput(AMBERHOME+AMBEREXEC+" -O -i equil5_"+self.sMName+".in -o equil5_"+self.sMName+".out -p "+self.sMName+"_solv_ions.prmtop -c equil4_"+self.sMName+".restrt -r equil5_"+self.sMName+".restrt -ref equil4_"+self.sMName+".restrt -x equil5_"+self.sMName+".mdcrd")[1]+"\n")
FEptraj.write("trajin equil5_"+self.sMName+".mdcrd 1 100 1\n")
if(self.check_quality() == False):
return False
print(" Equilibration in progress... 40%")
os.environ['CUDA_VISIBLE_DEVICES'] = self.sGPU_ID
FElog.write(commands.getstatusoutput(AMBERHOME+AMBEREXEC+" -O -i equil6_"+self.sMName+".in -o equil6_"+self.sMName+".out -p "+self.sMName+"_solv_ions.prmtop -c equil5_"+self.sMName+".restrt -r equil6_"+self.sMName+".restrt -ref equil4_"+self.sMName+".restrt -x equil6_"+self.sMName+".mdcrd")[1]+"\n")
FEptraj.write("trajin equil6_"+self.sMName+".mdcrd 1 100 1\n")
if(self.check_quality() == False):
return False
print(" Equilibration in progress... 45%")
os.environ['CUDA_VISIBLE_DEVICES'] = self.sGPU_ID
FElog.write(commands.getstatusoutput(AMBERHOME+AMBEREXEC+" -O -i equil7_"+self.sMName+".in -o equil7_"+self.sMName+".out -p "+self.sMName+"_solv_ions.prmtop -c equil6_"+self.sMName+".restrt -r equil7_"+self.sMName+".restrt -ref equil4_"+self.sMName+".restrt -x equil7_"+self.sMName+".mdcrd")[1]+"\n")
FEptraj.write("trajin equil7_"+self.sMName+".mdcrd 1 100 1\n")
if(self.check_quality() == False):
return False
print(" Equilibration in progress... 50%")
os.environ['CUDA_VISIBLE_DEVICES'] = self.sGPU_ID
FElog.write(commands.getstatusoutput(AMBERHOME+AMBEREXEC+" -O -i equil8_"+self.sMName+".in -o equil8_"+self.sMName+".out -p "+self.sMName+"_solv_ions.prmtop -c equil7_"+self.sMName+".restrt -r equil8_"+self.sMName+".restrt -ref equil4_"+self.sMName+".restrt -x equil8_"+self.sMName+".mdcrd")[1]+"\n")
FEptraj.write("trajin equil8_"+self.sMName+".mdcrd 1 100 1\n")
if(self.check_quality() == False):
return False
print(" Equilibration in progress... 55%")
os.environ['CUDA_VISIBLE_DEVICES'] = self.sGPU_ID
FElog.write(commands.getstatusoutput(AMBERHOME+AMBEREXEC+" -O -i equil9_"+self.sMName+".in -o equil9_"+self.sMName+".out -p "+self.sMName+"_solv_ions.prmtop -c equil8_"+self.sMName+".restrt -r equil9_"+self.sMName+".restrt -ref equil4_"+self.sMName+".restrt -x equil9_"+self.sMName+".mdcrd")[1]+"\n")
FEptraj.write("trajin equil9_"+self.sMName+".mdcrd 1 100 1\n")
if(self.check_quality() == False):
return False
print(" Equilibration in progress... 60%")
os.environ['CUDA_VISIBLE_DEVICES'] = self.sGPU_ID
FElog.write(commands.getstatusoutput(AMBERHOME+AMBEREXEC+" -O -i equil10_"+self.sMName+".in -o equil10_"+self.sMName+".out -p "+self.sMName+"_solv_ions.prmtop -c equil9_"+self.sMName+".restrt -r equil10_"+self.sMName+".restrt -ref equil4_"+self.sMName+".restrt -x equil10_"+self.sMName+".mdcrd")[1]+"\n")
FEptraj.write("trajin equil10_"+self.sMName+".mdcrd 1 100 1\n")
if(self.check_quality() == False):
return False
print(" Equilibration in progress... 65%")
os.environ['CUDA_VISIBLE_DEVICES'] = self.sGPU_ID