Hi Pengfei,
Thanks for the reply! I found the inconsistency and have solved the
problem, however a second problem has arisen! I have made a separate file
for the Fe2+ centre, and a single seperate file for the ligands surrounding
it (a nitrogen based bidentate ligand, a CO, a water and a Cl- ion).
However, the fingerprint files and .com files generated do not recognise
the Cl as Cl, but rather as carbon. Can I change the fingerprint files and
com files manually without any problems?
I will attach the .pdb and .mol2 files.
Thanks again for the help!
Dave
On 22 January 2016 at 17:10, Pengfei Li <ambermailpengfei.gmail.com> wrote:
> 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
>
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- application/octet-stream attachment: nika.in
Received on Mon Jan 25 2016 - 07:30:04 PST
