Hi Dave,
It maybe because there are too many files or the total size of the files is big in the former email that makes AMBER mail-list did not contain it. I will forward the sent mail to your personal email address.
Pengfei
> On Jan 29, 2016, at 4:20 AM, David Mayes <dm822.york.ac.uk> wrote:
>
> 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 <mailto: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> <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>
>> <mailto: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 <mailto: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 <mailto: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>>>
>> <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 <mailto:ambermailpengfei.gmail.com>>>>)?
>>>>>>
>>>>>> Pengfei
>>>>>>
>>>>>>> On Jan 22, 2016, at 8:25 AM, David Mayes <dm822.york.ac.uk <mailto:dm822.york.ac.uk> <mailto:
>> 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> <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>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org <mailto:AMBER.ambermd.org> <mailto:AMBER.ambermd.org <mailto:AMBER.ambermd.org>> <mailto:
>> 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>> <
>>>> 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
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>> <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>> <
>>>> 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 <http://lists.ambermd.org/mailman/listinfo/amber>>
>>>>
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Received on Fri Jan 29 2016 - 07:30:07 PST
