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

Mahendra B Thapa thapamb at mail.uc.edu
Tue Mar 17 22:39:17 PDT 2015

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
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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