Mahendra ThapaThank you for help,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 ?On Wed, Mar 18, 2015 at 5:08 AM, Thapa, Mahendra (thapamb) <thapamb@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@cgl.ucsf.edu
Subject: Re: [Chimera-users] How to get prmtop file corresponding to a pdb file
VictorKind regards,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.
2015-03-18 6:39 GMT+01:00 Mahendra B Thapa <thapamb@mail.uc.edu>:
_______________________________________________University of Cincinnati,OHMahendra ThapaThank you.Any help in this issue will be a good help for me.7] In reply log, 'Failure running ANTECHEMBER for residue HIS' seen.6] I got 'chimera error' - failure running ANTECHEMBER for residue HIS. Check reply log for details.5] In a pop up window 'specify net charge', I selected 'AMI-BCC' in charge method4] In a pop-up window 'Add charge', I selected 'AM1-BCC' in other residues, then clicked ok.3] No charges message appeared, then I clicked 'Assign charges'.2] In a pop-up window 'save file in chimera', I gave file name, say, aa.prmtop, then clicked save.1] tools -> Amber -> write prmtopDear Chimera users,To get Amber prmtop file corresponding to a pdb file using Chimera, I did the following steps:
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