Re: [AMBER] KeyError: 4018 for iron containing enzyme (prolyl hydroxylase)

From: Aashish Bhatt <aashish.ph16221.inst.ac.in>
Date: Wed, 3 Apr 2019 18:18:11 +0530

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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>
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Received on Wed Apr 03 2019 - 06:00:08 PDT
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