Hi Pengfei,
I can't thank you enough for your help! The only problem is I can't seem to
find any attachments on the email you sent.
Again, many thanks, and best wishes,
Dave
On 28 January 2016 at 18:08, Pengfei Li <ambermailpengfei.gmail.com> wrote:
> Hi Dave,
>
> Your case is special and the difficulty is bigger than a normal case.
>
> > On Jan 26, 2016, at 9:01 AM, David Mayes <dm822.york.ac.uk> wrote:
> >
> > Hi Pengfei,
> >
> > Seperating and treating as an ion seems to have worked, thanks!
> >
>
> That is great.
>
> > 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.
>
>
> In default, MCPB.py will only treat the metal-N/O/S/F/Cl/Br/I bond as bond
> but not metal-C/H bond.
>
> This is trying to prevent to detect unphysical bond in the low resolution
> structure.
>
> So there is some problem in your case. I have add a new variable in the
> MCPB.py program. You can download it from github (
> https://github.com/Amber-MD/pymsmt <https://github.com/Amber-MD/pymsmt>)
> and install it.
>
> The new variable is “bonded_atom_pairs”, based on which you can set the
> additional metal center bonding manually (In your case, it is the Metal-C
> bond). I have made corresponding modifications of your MCPB.py input file
> (see attachment).
>
> > I also don't see any H atoms in the .com and
> > .fingerprint outputs.
>
> This is because the H atoms in the ligand did not have the same residue
> number as the ligand so MCPB.py did not
> treat them in the same ligand, causing them not considered in the .com and
> .fingerprint files.
>
> I have made related modifications in the PDB file and regenerated the file
> by using pdb4amber. The new pdb file called nikaru_fixed_H_new.pdb. Related
> mol2 and frcmod files are updated.
>
> Please find the updated files attached. Using these files and the new
> MCPB.py program you can try to run the first step, it is no problem for me
> doing it in my computer.
>
>
>
> Pengfei
>
>
> >
> > Thanks again, and best wishes,
> >
> > Dave
> >
> > On 25 January 2016 at 23:49, Pengfei Li <ambermailpengfei.gmail.com
> <mailto: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 <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>>
> <mailto:
> >> 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 <mailto:
> 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 <mailto:AMBER.ambermd.org>
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber <
> http://lists.ambermd.org/mailman/listinfo/amber>
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org <mailto:AMBER.ambermd.org> <mailto:
> AMBER.ambermd.org <mailto:AMBER.ambermd.org>>
> >>>> http://lists.ambermd.org/mailman/listinfo/amber <
> http://lists.ambermd.org/mailman/listinfo/amber> <
> >> http://lists.ambermd.org/mailman/listinfo/amber <
> http://lists.ambermd.org/mailman/listinfo/amber>>
> >>>>
> >>> <LIG.mol2><nika.in
> >>> <nikaru_fixed_H.pdb>_______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org <mailto:AMBER.ambermd.org> <mailto:AMBER.ambermd.org
> <mailto:AMBER.ambermd.org>>
> >>> http://lists.ambermd.org/mailman/listinfo/amber <
> http://lists.ambermd.org/mailman/listinfo/amber> <
> >> http://lists.ambermd.org/mailman/listinfo/amber <
> http://lists.ambermd.org/mailman/listinfo/amber>>
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> >> http://lists.ambermd.org/mailman/listinfo/amber <
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> >>
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Received on Fri Jan 29 2016 - 01:30:04 PST
