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

Victor Muñoz chewaka.87 at gmail.com
Wed Mar 18 02:08:18 PDT 2015

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

Kind regards,


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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> Chimera-users at cgl.ucsf.edu
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