Thanks Aashish for the valuable information. I have corrected it and the
system is working fine.
On Wed, Apr 3, 2019 at 9:48 PM Aashish Bhatt <aashish.ph16221.inst.ac.in>
wrote:
> Dear Mahesh
>
> You choose wrong Fe id. In your 519b_fixed_H.pdb file, Fe id is 3475 and in
> the input file, you mentioned 4018.
> please again read the tutorial.
>
> Hope it will help you.
>
>
> Best regards
>
>
>
>
> On Wed, Apr 3, 2019 at 2:09 PM Mahesh kumar Teli <
> maheshkumar.teli.gmail.com>
> wrote:
>
> > Dear Amber users
> >
> > I am trying to parameterize iron for my system but could not solve the
> > following problem. I have checked for a solution on the amber community
> but
> > could not figure it out as the only suggestion mention was checking the
> > metal id. I have checked it and could not see any problem associated with
> > input files. I have attached the input file for your reference.
> >
> > [surendra.gpu MCPB]$ MCPB.py -i 5L9B.in -s 1
> > ******************************************************************
> > * 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 *
> > ******************************************************************
> > The input file you are using is : 5L9B.in
> > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> > The following is the input variable you have:
> > The variable ion_ids is : [4018]
> > The variable ion_info is : []
> > The variable ion_mol2files is : ['FE.mol2']
> > The variable original_pdb is : 5l9b_fixed_H.pdb
> > The variable add_bonded_pairs is : []
> > The variable add_redcrd is : 0
> > The variable additional_resids is : []
> > The variable anglefc_avg is : 0
> > The variable bondfc_avg is : 0
> > The variable chgfix_resids is : []
> > The variable cut_off is : 2.8
> > The variable force_field is : ff14SB
> > The variable frcmod_files is : ['AKG.frcmod']
> > The variable gaff is : 1
> > The variable group_name is : 5L9B
> > The variable ion_paraset is : CM (Only for nonbonded model)
> > The variable large_opt is : 1
> > The variable lgmodel_chg is : -99
> > The variable lgmodel_spin is : -99
> > -99 means program will assign a charge automatically.
> > The variable naa_mol2files is : ['WAT.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 : -99
> > The variable smmodel_spin is : -99
> > -99 means program will assign a charge automatically.
> > The variable software_version is : g03
> > The variable sqm_opt is : 0
> > The variable water_model is : TIP3P
> > The variable xstru is : 0
> > Traceback (most recent call last):
> > File "/home/surendra/anaconda2/bin/MCPB.py", line 577, in <module>
> > addbpairs)
> > File
> >
> >
> "/home/surendra/anaconda2/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py",
> > line 51, in get_ms_resnames
> > resid = mol.atoms[i].resid
> > KeyError: 4018
> >
> > Thank you
> >
> > Best Regards
> > Mahesh
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Apr 03 2019 - 19:30:02 PDT
