[AMBER] Regarding error in MCPB.py

From: dhaval patel <pateldhaval.in.gmail.com>
Date: Sun, 2 Sep 2018 14:48:23 +0530

Hello Users,

I am trying to use MCPB.py to generate parameters for Ru based ligand. I am
getting following error in Step no 3, below you can find the same.
Can anyone help me to fix this issue:

*MCPB.py -i 4MVF.in -s
Welcome to use the MCPB.py program
** Version 4.0
** Author: Pengfei Li
** Merz Research Group
** Michigan State University
** AND
** Hammes-Schiffer Research Group
** UIUC and Yale
input file you are using is :
following is the input variable you have:The variable ion_ids is :
[7446]The variable ion_info is : []The variable ion_mol2files is :
['RU.mol2']The variable original_pdb is : 4MVF_VIP_renum.pdbThe variable
add_bonded_pairs is : []The variable add_redcrd is : 0The variable
additional_resids is : []The variable anglefc_avg is : 0The variable
bondfc_avg is : 0The variable chgfix_resids is : []The variable cut_off
is : 2.8The variable force_field is : ff14SBThe variable frcmod_files is
: ['VIP.frcmod']The variable gaff is : 1The variable group_name is :
4MVF_VIPThe variable ion_paraset is : CM (Only for nonbonded model)The
variable large_opt is : 0The variable lgmodel_chg is : -99The variable
lgmodel_spin is : -99 -99 means program will assign a charge
automatically.The variable naa_mol2files is : ['VIP.mol2']The variable
scale_factor is : 1.0 ATTENTION: This is the scale factor of
frequency. The force constants will be scaled by multiplying
the square of scale_factor.The variable smmodel_chg is :
-99The variable smmodel_spin is : -99 -99 means program will
assign a charge automatically.The variable software_version is : g09The
variable sqm_opt is : 0The variable water_model is : TIP3PThe variable
xstru is :
**======================RESP Charge
the 1st stage resp charge fitting input file...***Generating the 2nd stage
resp charge fitting input file...***Doing the RESP charge
models==========================***Check the large model...Good. The
charges and atom numbers are match for the large model.Good. There are 71
atoms in the large model.***Check the standard model...Traceback (most
recent call last): File "/home/dhaval/Desktop/amber18//bin/MCPB.py", line
684, in <module> premol2fs, mcresname, 1, chgfix_resids, g0x, lgchg)
line 520, in resp_fitting raise pymsmtError('Error: the charges and atom
numbers are mismatch 'pymsmt.exp.pymsmtError: Error: the charges and atom
numbers are mismatch for the standard model!*

Sincerely yours,
Dhaval Patel | PhD
The M. S. University of Baroda, Vadodara.
Lab: Biophysics & Structural Biology,
Indian Institute of Advanced Research,
Gujarat, INDIA. +91 9925450504
pateldhaval.in.gmail.com; dhaval.iiar.res.in
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Received on Sun Sep 02 2018 - 02:30:02 PDT
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