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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Received on Tue Sep 01 2015 - 21:00:03 PDT
