def getEnergies(template):
cmd = template % cmdDict
pdebug(cmd)
out = _getoutput(cmd)
out = out.split('\n')[-nEner:]
dictEner = {}
for item in out:
k, v = item.replace(' Dih.', '_Dih.').replace(
' (SR)', '_(SR)').replace('c En.', 'c_En.').replace(
' (bar)', '_(bar)').replace('l E', 'l_E').split()[:2]
v = eval(v)
dictEner[k] = v
if 'Dih.' in k or 'Bell.' in k:
if 'Dihedral P+I' in list(dictEner.keys()):
dictEner['Dihedral P+I'] = dictEner['Dihedral P+I'] + v
else:
dictEner['Dihedral P+I'] = v
if 'Coulomb' in k or 'LJ' in k:
if 'TotalNonBonded' in list(dictEner.keys()):
dictEner['TotalNonBonded'] = dictEner['TotalNonBonded'] + v
else:
dictEner['TotalNonBonded'] = v
dictEner['Total_Bonded'] = dictEner.get('Potential') - dictEner.get(
'TotalNonBonded')
return dictEner
def getEnergies(template):
cmd = template % cmdDict
pdebug(cmd)
out = _getoutput(cmd)
out = out.split('\n')[-nEner:]
dictEner = {}
for item in out:
k, v = item.replace(' Dih.', '_Dih.').replace(' (SR)', '_(SR)').replace('c En.', 'c_En.').replace(' (bar)', '_(bar)').replace('l E', 'l_E').split()[:2]
v = eval(v)
dictEner[k] = v
if 'Dih.' in k or 'Bell.' in k:
if 'Dihedral P+I' in list(dictEner.keys()):
dictEner['Dihedral P+I'] = dictEner['Dihedral P+I'] + v
else:
dictEner['Dihedral P+I'] = v
if 'Coulomb' in k or 'LJ' in k:
if 'TotalNonBonded' in list(dictEner.keys()):
dictEner['TotalNonBonded'] = dictEner['TotalNonBonded'] + v
else:
dictEner['TotalNonBonded'] = v
dictEner['Total_Bonded'] = dictEner.get('Potential') - dictEner.get('TotalNonBonded')
return dictEner
def build_residues_tleap():
"""Build residues tripeptides with tleap and minimise with sander"""
mdin = '''Minimization\n&cntrl\nimin=1, maxcyc=200, ntmin=2, ntb=0, igb=0,cut=999,/\n'''
open('mdin', 'w').writelines(mdin)
seqi = aa_dict.keys()
for aai in seqi:
#if aai != 'H': continue
aai3 = 3 * aai
res = aa_dict.get(aai).upper()
res1 = res
leapDict = {'amberff' : amberff, 'res' : res, 'aai3' : aai3, 'res1':res1}
tleapin = genPdbTemplate % leapDict
open('tleap.in', 'w').writelines(tleapin)
cmd = "%s -f tleap.in" % (tleapExe)
_getoutput(cmd)
#cmd = "%s -O; %s < restrt > %s.pdb; mv mdinfo %s.mdinfo" % (sanderExe, ambpdbExe, aai3, aai3) # -i mdin -o mdout -p prmtop -c inpcrd" % (sanderExe)
cmd = "%s -O; %s < restrt > %s.pdb" % (sanderExe, ambpdbExe, aai3)
_getoutput(cmd)
_getoutput('rm -f mdout mdinfo mdin restrt tleap.in prmtop inpcrd leap.log')
def build_residues_tleap():
"""Build residues tripeptides with tleap and minimise with sander"""
mdin = '''Minimization\n&cntrl\nimin=1, maxcyc=200, ntmin=2, ntb=0, igb=0,cut=999,/\n'''
open('mdin', 'w').writelines(mdin)
seqi = aa_dict.keys()
for aai in seqi:
#if aai != 'H': continue
aai3 = 3 * aai
res = aa_dict.get(aai).upper()
res1 = res
leapDict = {'amberff': amberff, 'res': res, 'aai3': aai3, 'res1': res1}
tleapin = genPdbTemplate % leapDict
open('tleap.in', 'w').writelines(tleapin)
cmd = "%s -f tleap.in" % (tleapExe)
_getoutput(cmd)
#cmd = "%s -O; %s < restrt > %s.pdb; mv mdinfo %s.mdinfo" % (sanderExe, ambpdbExe, aai3, aai3) # -i mdin -o mdout -p prmtop -c inpcrd" % (sanderExe)
cmd = "%s -O; %s < restrt > %s.pdb" % (sanderExe, ambpdbExe, aai3)
_getoutput(cmd)
_getoutput(
'rm -f mdout mdinfo mdin restrt tleap.in prmtop inpcrd leap.log')
def calcGmxPotEnerDiff(res):
def getEnergies(template):
cmd = template % cmdDict
pdebug(cmd)
out = _getoutput(cmd)
out = out.split('\n')[-nEner:]
dictEner = {}
for item in out:
k, v = item.replace(' Dih.', '_Dih.').replace(' (SR)', '_(SR)').replace('c En.', 'c_En.').replace(' (bar)', '_(bar)').replace('l E', 'l_E').split()[:2]
v = eval(v)
dictEner[k] = v
if 'Dih.' in k or 'Bell.' in k:
if 'Dihedral P+I' in list(dictEner.keys()):
dictEner['Dihedral P+I'] = dictEner['Dihedral P+I'] + v
else:
dictEner['Dihedral P+I'] = v
if 'Coulomb' in k or 'LJ' in k:
if 'TotalNonBonded' in list(dictEner.keys()):
dictEner['TotalNonBonded'] = dictEner['TotalNonBonded'] + v
else:
dictEner['TotalNonBonded'] = v
dictEner['Total_Bonded'] = dictEner.get('Potential') - dictEner.get('TotalNonBonded')
return dictEner
os.chdir(tmpDir)
nEner = 9 # number of energy entries from g_energy
tEner = ' '.join([str(x) for x in range(1, nEner + 1)])
open('SPE.mdp', 'w').writelines(spe_mdp)
cmdDict = {'pdb2gmx':pdb2gmx, 'grompp':grompp, 'mdrun':mdrun, 'res':res,
'g_energy':g_energy, 'tEner':tEner, 'water':water, 'gmxdump':gmxdump}
# calc Pot Ener for aXXX.pdb (AMB_GMX)
template = '''%(pdb2gmx)s -ff amber99sb -f a%(res)s.pdb -o a%(res)s_.pdb -p a%(res)s.top %(water)s
%(grompp)s -c a%(res)s_.pdb -p a%(res)s.top -f SPE.mdp -o a%(res)s.tpr -pp a%(res)sp.top
%(mdrun)s -v -deffnm a%(res)s
echo %(tEner)s | %(g_energy)s -f a%(res)s.edr
'''
dictEnerAMB = getEnergies(template)
#print(dictEnerAMB)
#calc Pot Ener for agXXX.acpype/agXXX.pdb (ACPYPE_GMX)
template = '''%(grompp)s -c ag%(res)s.acpype/ag%(res)s_NEW.pdb -p ag%(res)s.acpype/ag%(res)s_GMX.top -f SPE.mdp -o ag%(res)s.tpr -pp ag%(res)sp.top
%(mdrun)s -v -deffnm ag%(res)s
echo %(tEner)s | %(g_energy)s -f ag%(res)s.edr
'''
dictEnerACPYPE = getEnergies(template)
#print(dictEnerACPYPE)
order = ['LJ-14', 'LJ_(SR)', 'Coulomb-14', 'Coulomb_(SR)', 'TotalNonBonded', 'Potential', 'Angle', 'Bond', 'Proper_Dih.', 'Improper_Dih.', 'Dihedral P+I', 'Total_Bonded'] #sorted(dictEnerAMB.items())
for k in order:
v = dictEnerAMB.get(k)
v2 = dictEnerACPYPE.get(k)
rerror = error(v2, v)
if rerror > 0.1:
print("%15s %.3f %5.6f x %5.6f" % (k, rerror, v2, v))
else:
print("%15s %.3f" % (k, rerror))
cmd = "%(gmxdump)s -s a%(res)s.tpr" % cmdDict
amb = _getoutput(cmd)
cmd = "%(gmxdump)s -s ag%(res)s.tpr" % cmdDict
acp = _getoutput(cmd)
#dihAmb = [x.split(']=')[-1] for x in amb.splitlines() if ('PIDIHS' in x or 'PDIHS' in x) and 'functype' in x ]
#dihAcp = [x.split(']=')[-1] for x in acp.splitlines() if ('PIDIHS' in x or 'PDIHS' in x) and 'functype' in x ]
dihAmb = [x.split('PIDIHS')[-1][2:] for x in amb.splitlines() if ('PIDIHS' in x)]
dihAcp = [x.split('PIDIHS')[-1][2:] for x in acp.splitlines() if ('PIDIHS' in x)]
dAcp = set(dihAcp).difference(set(dihAmb))
dAmb = set(dihAmb).difference(set(dihAcp))
rAcp = [' '.join(reversed(x.split())) for x in dAcp]
rAmb = [' '.join(reversed(x.split())) for x in dAmb]
ddAmb = sorted(dAmb.difference(rAcp))
ddAcp = sorted(dAcp.difference(rAmb))
if ddAmb: print('IDIH: Amb diff Acp', ddAmb)
if ddAcp: print('IDIH: Acp diff Amb', ddAcp)
return dihAmb, dihAcp
listRes.sort()
for resFile in listRes:
res, ext = os.path.splitext(resFile) # eg. res = 'AAA'
#if res != 'RRR': continue
if len(resFile) == 7 and ext == ".pdb" and resFile[:3].isupper():
print("\nFile %s : residue %s" % (resFile, aa_dict[res[0]].upper()))
_pdb = createOldPdb2(resFile) # using my own dict
apdb = createAmberPdb3(_pdb) # create file aAAA.pdb with NXXX, CXXX
# from ogpdb to amber pdb and top
agpdb = 'ag%s.pdb' % res # output name
agtop = 'ag%s.top' % res
cmd = ' %s -f %s -o %s -p %s -ff amber99sb %s' % (pdb2gmx, apdb, agpdb, agtop, water)
pdebug(cmd)
out = _getoutput(cmd)
#print(out)
#parseOut(out)
# acpype on agpdb file
fixRes4Acpype(agpdb)
cv = None
#cmd = "%s -dfi %s -c %s -a %s" % (acpypeExe, agpdb, cType, ffType)
if res in ['JJJ', 'RRR'] and cType == 'bcc': cv = 3 #cmd += ' -n 3' # acpype failed to get correct charge
mol = ACTopol(agpdb, chargeType = cType, atomType = ffType, chargeVal = cv,
debug = False, verbose = debug, gmx45 = True)
mol.createACTopol()
mol.createMolTopol()
#out = commands.getstatusoutput(cmd)
#parseOut(out[1])
def calcGmxPotEnerDiff(res):
def getEnergies(template):
cmd = template % cmdDict
pdebug(cmd)
out = _getoutput(cmd)
out = out.split('\n')[-nEner:]
dictEner = {}
for item in out:
k, v = item.replace(' Dih.', '_Dih.').replace(
' (SR)', '_(SR)').replace('c En.', 'c_En.').replace(
' (bar)', '_(bar)').replace('l E', 'l_E').split()[:2]
v = eval(v)
dictEner[k] = v
if 'Dih.' in k or 'Bell.' in k:
if 'Dihedral P+I' in list(dictEner.keys()):
dictEner['Dihedral P+I'] = dictEner['Dihedral P+I'] + v
else:
dictEner['Dihedral P+I'] = v
if 'Coulomb' in k or 'LJ' in k:
if 'TotalNonBonded' in list(dictEner.keys()):
dictEner['TotalNonBonded'] = dictEner['TotalNonBonded'] + v
else:
dictEner['TotalNonBonded'] = v
dictEner['Total_Bonded'] = dictEner.get('Potential') - dictEner.get(
'TotalNonBonded')
return dictEner
os.chdir(tmpDir)
nEner = 9 # number of energy entries from g_energy
tEner = ' '.join([str(x) for x in range(1, nEner + 1)])
open('SPE.mdp', 'w').writelines(spe_mdp)
cmdDict = {
'pdb2gmx': pdb2gmx,
'grompp': grompp,
'mdrun': mdrun,
'res': res,
'g_energy': g_energy,
'tEner': tEner,
'water': water,
'gmxdump': gmxdump
}
# calc Pot Ener for aXXX.pdb (AMB_GMX)
template = '''%(pdb2gmx)s -ff amber99sb -f a%(res)s.pdb -o a%(res)s_.pdb -p a%(res)s.top %(water)s
%(grompp)s -c a%(res)s_.pdb -p a%(res)s.top -f SPE.mdp -o a%(res)s.tpr -pp a%(res)sp.top
%(mdrun)s -v -deffnm a%(res)s
echo %(tEner)s | %(g_energy)s -f a%(res)s.edr
'''
dictEnerAMB = getEnergies(template)
#print(dictEnerAMB)
#calc Pot Ener for agXXX.acpype/agXXX.pdb (ACPYPE_GMX)
template = '''%(grompp)s -c ag%(res)s.acpype/ag%(res)s_NEW.pdb -p ag%(res)s.acpype/ag%(res)s_GMX.top -f SPE.mdp -o ag%(res)s.tpr -pp ag%(res)sp.top
%(mdrun)s -v -deffnm ag%(res)s
echo %(tEner)s | %(g_energy)s -f ag%(res)s.edr
'''
dictEnerACPYPE = getEnergies(template)
#print(dictEnerACPYPE)
order = [
'LJ-14', 'LJ_(SR)', 'Coulomb-14', 'Coulomb_(SR)', 'TotalNonBonded',
'Potential', 'Angle', 'Bond', 'Proper_Dih.', 'Improper_Dih.',
'Dihedral P+I', 'Total_Bonded'
] #sorted(dictEnerAMB.items())
for k in order:
v = dictEnerAMB.get(k)
v2 = dictEnerACPYPE.get(k)
rerror = error(v2, v)
if rerror > 0.1:
print("%15s %.3f %5.6f x %5.6f" % (k, rerror, v2, v))
else:
print("%15s %.3f" % (k, rerror))
cmd = "%(gmxdump)s -s a%(res)s.tpr" % cmdDict
amb = _getoutput(cmd)
cmd = "%(gmxdump)s -s ag%(res)s.tpr" % cmdDict
acp = _getoutput(cmd)
#dihAmb = [x.split(']=')[-1] for x in amb.splitlines() if ('PIDIHS' in x or 'PDIHS' in x) and 'functype' in x ]
#dihAcp = [x.split(']=')[-1] for x in acp.splitlines() if ('PIDIHS' in x or 'PDIHS' in x) and 'functype' in x ]
dihAmb = [
x.split('PIDIHS')[-1][2:] for x in amb.splitlines() if ('PIDIHS' in x)
]
dihAcp = [
x.split('PIDIHS')[-1][2:] for x in acp.splitlines() if ('PIDIHS' in x)
]
dAcp = set(dihAcp).difference(set(dihAmb))
dAmb = set(dihAmb).difference(set(dihAcp))
rAcp = [' '.join(reversed(x.split())) for x in dAcp]
rAmb = [' '.join(reversed(x.split())) for x in dAmb]
ddAmb = sorted(dAmb.difference(rAcp))
ddAcp = sorted(dAcp.difference(rAmb))
if ddAmb: print('IDIH: Amb diff Acp', ddAmb)
if ddAcp: print('IDIH: Acp diff Amb', ddAcp)
return dihAmb, dihAcp
#if res != 'RRR': continue
if len(resFile) == 7 and ext == ".pdb" and resFile[:3].isupper():
print("\nFile %s : residue %s" %
(resFile, aa_dict[res[0]].upper()))
_pdb = createOldPdb2(resFile) # using my own dict
apdb = createAmberPdb3(
_pdb) # create file aAAA.pdb with NXXX, CXXX
# from ogpdb to amber pdb and top
agpdb = 'ag%s.pdb' % res # output name
agtop = 'ag%s.top' % res
cmd = ' %s -f %s -o %s -p %s -ff amber99sb %s' % (
pdb2gmx, apdb, agpdb, agtop, water)
pdebug(cmd)
out = _getoutput(cmd)
#print(out)
#parseOut(out)
# acpype on agpdb file
fixRes4Acpype(agpdb)
cv = None
#cmd = "%s -dfi %s -c %s -a %s" % (acpypeExe, agpdb, cType, ffType)
if res in ['JJJ', 'RRR'] and cType == 'bcc':
cv = 3 #cmd += ' -n 3' # acpype failed to get correct charge
mol = ACTopol(agpdb,
chargeType=cType,
atomType=ffType,
chargeVal=cv,
debug=False,
verbose=debug,
