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>
>>>>
>>>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>>
>>>>
>>> <LIG.mol2><nika.in
>>> <nikaru_fixed_H.pdb>_______________________________________________
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Received on Thu Jan 28 2016 - 09:30:04 PST
