Hi David,
It seems there is inconsistency between your PDB file and mol2 file for the ligand. Can you send me these two files in an independent email (to ambermailpengfei.gmail.com <mailto:ambermailpengfei.gmail.com>)?
Pengfei
> On Jan 22, 2016, at 8:25 AM, David Mayes <dm822.york.ac.uk> wrote:
>
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 22 2016 - 08:30:05 PST
