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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Received on Mon Jan 25 2016 - 15:00:04 PST
