Hi Pengfei,
Seperating and treating as an ion seems to have worked, thanks!
Unfortunately now I do not see the carbon monoxide molecule in any of the
.com or .fingerprint files. I've tried seperating it out and treating it as
a seperate ligand. I also don't see any H atoms in the .com and
.fingerprint outputs.
Thanks again, and best wishes,
Dave
On 25 January 2016 at 23:49, Pengfei Li <ambermailpengfei.gmail.com> wrote:
> Hi David,
>
> For the Cl- ion, you can treat it in the similar way as treating the Fe2+
> ion. You need to separate it as an independent residue with residue name as
> "CL" and atom name as "CL". And then the program will recognize it as a Cl-
> ion. Please let me know whether it works.
>
> Pengfei
>
> > On Jan 25, 2016, at 10:04 AM, David Mayes <dm822.york.ac.uk> wrote:
> >
> > 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
> <mailto: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> <mailto:
> 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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> >>
> > <LIG.mol2><nika.in
> ><nikaru_fixed_H.pdb>_______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber <
> http://lists.ambermd.org/mailman/listinfo/amber>
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Received on Tue Jan 26 2016 - 06:30:04 PST
