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@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@cgl.ucsf.edu
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users