Hi Shilpa,
Can you send me the PDB file you used for the modeling? I can help to do a
check. You can send me a private email if needed.
Best,
Pengfei
2015-09-01 23:42 GMT-04:00 Sushi Shilpa <sushishilpa.gmail.com>:
> Dear amber users,
>
> I am following mcpb.py tutorial for metalloprotien simulation, while using
> the command MCPB.py -i comp.in -s 1a, I got a warning message mentioned
> below, could you please help me to solve this issue.
>
> /usr/lib/python2.7/dist-packages/numpy/oldnumeric/__init__.py:11:
> ModuleDeprecationWarning: The oldnumeric module will be dropped in Numpy
> 1.9
> warnings.warn(_msg, ModuleDeprecationWarning)
>
>
>
> ******************************************************************
> * Welcome to use MCPB.py program *
> * Version 1.0 Beta2 *
> * Pre-release Date: June 26 2015 *
> * Author: Pengfei Li *
> * Merz Research Group *
> * Michigan State University *
> * All Rights Reserved *
> ******************************************************************
>
>
>
> The input file you are using is : comp.in
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> The following is the input variable you have:
> The variable original_pdb is : cdc25_H.pdb
> The variable ion_ids is : [4018]
> The variable ion_mol2files is : ['po4_pre.mol2']
> The variable additional_resids is : []
> The variable group_name is : comp
> The variable cut_off is : 2.8
> The variable chgfix_resids is : []
> The variable scmodel_chg is : -99
> -99 means program will assign a charge automatically.
> The variable lgmodel_chg is : -99
> -99 means program will assign a charge automatically.
> The variable software_version is : g03
> The variable sqm_opt is : 0
> The variable large_opt is : 0
> The variable force_field is : ff14SB
> The variable gaff is : 1
> The variable frcmodfs is : []
> The variable scale_factor is : 1.0
> Attention: The force constants will be scaled by
> multiplying the square of scale_factor.
> The variable bondfc_avg is : 0
> The variable anglefc_avg is : 0
> The variable naa_mol2files is : []
> The variable software_version is : g03
> The variable water_model is : TIP3P
> The variable ion_paraset is : CM (Only for nonbonded model)
> The variable ion_info is : []
> Traceback (most recent call last):
> File "/home/camp/Desktop/Amber14/amber14/bin/MCPB.py", line 491, in
> <module>
> mcresname0, mcresname = get_ms_resnames(orpdbf, ionids, cutoff)
> File
>
> "/home/camp/Desktop/Amber14/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py",
> line 46, in get_ms_resnames
> resid = mol.atoms[i].resid
> KeyError: 4018
>
>
>
>
> Thanks in advance.
>
>
> Regards
>
> Shilpa T
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>
--
Pengfei Li
Ph.D. Candidate
Merz Research Group
Department of Chemistry
Michigan State University
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Received on Wed Sep 02 2015 - 19:00:03 PDT
