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

[Mahendra B Thapa]

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
>>
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>>
>>
>
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