[Chimera-users] FW: How to get prmtop file corresponding to a pdb file

Victor Muñoz chewaka.87 at gmail.com
Wed Mar 18 05:12:12 PDT 2015


Dear Mahendra,

Yes, I would say you should do that. Try converting all the atom names from
whatever name they have to the appropriate one for AMBER. Pay special
attention to the terminal residues, as there may be some differences on the
atom names depending on how you generated the PDB files.

Kind regards,

Victor

2015-03-18 13:04 GMT+01:00 Mahendra B Thapa <thapamb at mail.uc.edu>:

> Dear Dr. Victor,
>
> Thank you for reminding me about the protonation state of HIS. As a trial,
> I changed all HIS to HID and again repeated my previous steps. This time, I
> got some python track back errors. I suspect the source of error could be
> the initial pdb file which I used in chimera ; the pdb file was obtained
> from other software (like online server), so some atom names were different
> from that of AMBER. My goal was to get AMBER prmtop corresponding to pdb
> files which were generated by  programs other than AMBER so that I could
> use ambertools. So, may I need to convert all such pdb files compatible
> with amber pdb format ?
>
> Thank you for help,
> Mahendra Thapa
>
>
> On Wed, Mar 18, 2015 at 5:08 AM, Thapa, Mahendra (thapamb) <
> thapamb at mail.uc.edu> wrote:
>
>>
>> ------------------------------
>> *From:* Victor Muñoz
>> *Sent:* Wednesday, March 18, 2015 3:08:18 AM (UTC-06:00) Central America
>> *To:* Thapa, Mahendra (thapamb)
>> *Cc:* chimera-users at cgl.ucsf.edu
>> *Subject:* Re: [Chimera-users] How to get prmtop file corresponding to a
>> pdb file
>>
>>    Dear Mahendra,
>>
>>  The error is due to HIS not being the standard residue name for
>> Histidine in the Amber force field. In Amber, histidine residues are named
>> either HIE, HID or HIP depending on their protonation state (
>> http://ambermd.org/Questions/HIS.html). Change the name of the
>> histidines on the PDB file accordingly to their protonation state and it
>> should work fine.
>>
>>  Kind regards,
>>
>>  Victor
>>
>> 2015-03-18 6:39 GMT+01:00 Mahendra B Thapa <thapamb at mail.uc.edu>:
>>
>>>       Dear Chimera users,
>>>
>>>  To get *Amber prmtop file* corresponding to a *pdb file using Chimera*,
>>> I did the following steps:
>>>  1] tools -> Amber -> write prmtop
>>>  2] In a pop-up window 'save file in chimera', I gave file name, say,
>>> aa.prmtop, then clicked save.
>>>  3] No charges message appeared, then I clicked 'Assign charges'.
>>>  4] In a pop-up window 'Add charge', I selected 'AM1-BCC' in other
>>> residues, then clicked ok.
>>>  5] In a pop up window 'specify net charge', I selected 'AMI-BCC' in
>>> charge method
>>>  6] I got 'chimera error' - failure running ANTECHEMBER for residue HIS.
>>> Check reply log for details.
>>>  7] In reply log, '*Failure running ANTECHEMBER for residue HIS*' seen.
>>>
>>>  Any help in this issue will be a good help for me.
>>>
>>>  Thank you.
>>>  Mahendra Thapa
>>>  University of Cincinnati,OH
>>>
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>
>>>
>>
>
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