Hello,
I've been trying to run MCPB.py nonbonded model to parameterise VIM-2 in complex with L8J (PDB ID 6O5T) with two zinc files in its active site.
I've been following this tutorial <
http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm> but only running the large model MK charge calculation, as I want to run the nonbonded model with refitting charges.
As per the Amber22 manual, I am following the MCPB.py steps 1m -> 3b -> 4n1.
Running step 3b takes in the old ZN mol2 files and refits the charge from +2 to ~0.79 and ~1.08, according to the DFT output file of the population analysis.
However, when running step 4n1, I get the following error:
Traceback (most recent call last):
File "/home/jguven/Software/amber22/bin/MCPB.py", line 712, in <module>
gene_leaprc(gname, orpdbf, fipdbf, stpdbf, stfpf, ionids, ionmol2fs,
File "/home/jguven/Software/amber22/lib/python3.10/site-packages/pymsmt/mcpb/amber_modeling.py", line 201, in gene_leaprc
frcmodf = get_frcmod_fname(element, chg, watermodel, paraset)
File "/home/jguven/Software/amber22/lib/python3.10/site-packages/pymsmt/mcpb/amber_modeling.py", line 108, in get_frcmod_fname
return frcmodf
UnboundLocalError: local variable 'frcmodf' referenced before assignment
I looked at the file amber_modeling.py and found this in lines 194-203:
#----------------------Generate the lib file and get the frcmod file name
if model == 2:
for ionmol2f in ionmol2fs:
ionmol, ionatids, ionresids = get_atominfo(ionmol2f)
for i in ionatids:
element = ionmol.atoms[i].element
chg = int(ionmol.atoms[i].charge)
frcmodf = get_frcmod_fname(element, chg, watermodel, paraset)
if frcmodf not in frcmodfs:
frcmodfs.append(frcmodf)
Since the ionmol variable is read in from get_atominfo which reads in the .mol2 files of the zinc ions, these are now ~0.79 and ~1.08 for my case. Since the above code block converts the ionmol.atoms[i].charge to an integer, this sets the charge to 0 and 1 respectively.
Thus, in get_frcmod_fname():
# Choose the correct frcmod file for the ion
if watermodel in ['tip3p', 'spce', 'tip4pew']:
#For monovalent ions
if charge in [-1, 1]:
frcmodf = 'frcmod.ions1lm_'
if paraset in ['hfe', 'cm', '12_6']:
frcmodf = frcmodf + '126_' + watermodel
elif paraset == 'iod':
frcmodf = frcmodf + 'iod'
elif paraset == '12_6_4':
frcmodf = frcmodf + '1264_' + watermodel
#For +2, +3, and +4 ions
elif charge in [2, 3, 4]:
frcmodf = 'frcmod.ions234lm_'
if paraset == 'hfe':
frcmodf = frcmodf + 'hfe_' + watermodel
elif paraset == 'iod':
frcmodf = frcmodf + 'iod_' + watermodel
elif paraset == '12_6_4':
frcmodf = frcmodf + '1264_' + watermodel
elif paraset in ['cm', '12_6']:
frcmodf = frcmodf + '126_' + watermodel
elif watermodel in ['opc3', 'opc', 'fb3', 'fb4']:
frcmodf = 'frcmod.ionslm_'
if paraset == 'hfe':
frcmodf = frcmodf + 'hfe_' + watermodel
if paraset in ['cm', '12_6']:
frcmodf = frcmodf + '126_' + watermodel
elif paraset == 'iod':
frcmodf = frcmodf + 'iod_' + watermodel
elif paraset == '12_6_4':
frcmodf = frcmodf + '1264_' + watermodel
return frcmodf
The frcmodf file is not defined for a charge of 0, which causes the error.
Am I doing something wrong in the workflow, or is this a bug in the code? I've uploaded some of my files for convenience.
Many thanks in advance.
Kind regards,
Jasmin Güven
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.
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Received on Fri May 05 2023 - 05:30:02 PDT
