Hi David, Pengfei and Amber community,
Could anyone point me to AMBER parameters/papers for modeling iron/ligand (nitrogen ligand) parameters?
I ask like this because I see some recent discussions that mentioned iron and I’m about to start designing some iron binding catalysts.
Thanks,
Christian Schafmeister
Professor
Chemistry Department
Temple University
meister.temple.edu
> 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!
>
> 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
>>>>> _______________________________________________
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>>>>> 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 Tue Jan 26 2016 - 07:00:03 PST
