Hi,
I'm currently trying to adapt the MCPB.py tutorial to an artificial
metalloenzyme, and I'm getting stuck.
$ MCPB.py -i xyz.in -s 1a
******************************************************************
* Welcome to use MCPB.py program *
* Author: Pengfei Li *
* Merz Research Group *
* Michigan State University *
* All Rights Reserved *
******************************************************************
The input file you are using is : xyz.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
The following is the input variable you have:
The variable original_pdb is : xyz_fixed_H.pdb
The variable ion_ids is : [7864]
The variable ion_mol2files is : ['FE.mol2']
The variable group_name is : xyz
The variable cut_off is : 2.8
The variable ionchg_fixation is : 0
The variable gau_version is : g03
The variable sqm_opt is : 0
The variable force_field is : ff14SB
The variable gaff is : 1
The variable frcmodfs is : ['LIG.frcmod']
The variable naa_mol2files is : ['LIG.mol2']
The variable water_model is : TIP3P
The variable ion_paraset is : CM (Only for nonbonded model)
The variable ion_info is : []
******************************************************************
* *
*=======================Metal Site Information===================*
* *
******************************************************************
***Selected Metal ion FE2 is atom 7864 in residue 499-FE2
500-LIG.NAD is in 2.8 Angstrom of 500-LIG.NAD
500-LIG.NAE is in 2.8 Angstrom of 500-LIG.NAE
500-LIG.OXT is in 2.8 Angstrom of 500-LIG.OXT
500-LIG.N is in 2.8 Angstrom of 500-LIG.N
500-LIG.NAM is in 2.8 Angstrom of 500-LIG.NAM
***The following residues are in the Metal Site:
Residue 499-FE2
Residue 500-LIG
***The large model contains the following residues:
[499, 500]
******************************************************************
* *
*=======================Building models==========================*
* *
******************************************************************
***Creating the sidechain model...
It contains the residue 499-FE2
It contains the residue 500-LIG
Totally there are 25 atoms in the sidechain model.
Totally there are 145 electrons in the sidechain model.
***Creating the standard model...
It contains the residue 499-FE2
It contains the residue 500-LIG
Traceback (most recent call last):
File "/usr/local/PROGS/AMBER/amber14/bin/MCPB.py", line 419, in <module>
watermodel, 2, sqmopt)
File
"/usr/local/PROGS/AMBER/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py",
line 1164, in gene_model_files
libdict, autoattyp)
File
"/usr/local/PROGS/AMBER/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py",
line 355, in build_standard_model
attype = libdict[resname + '-' + atname][0]
KeyError: 'LIG-NAD'
The Fe is coordinated by two sp2 nitrogen atoms in a planar 5 membered
ring. The ring is part of a ligand that is bound by electrostatics to the
protein.
I followed the tutorial, and have separated the Fe to its own .pdb file, as
well as assigning the ligand its own .pdb file, before recombining the 3
.pdb files to xyz_fixed_H.pdb
Thanks in advance,
David
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Received on Fri Jan 22 2016 - 05:30:09 PST
