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

Eric Pettersen pett at cgl.ucsf.edu
Wed Mar 18 11:32:30 PDT 2015


Hi Mahendra,
	If your PDB file has standard PDB atom names, then Chimera will have no problem deciding if the HIS residues should be HID (delta protonated), HIE (epsilon protonated), or HIP (both) for Amber purposes.  Apparently your file does not have PDB standard names throughout.  In particular, the proton names in your HIS residues must be non-standard.  Chimera makes the HIS decision based on whether your residue has an HD1 proton, an HE2 proton, or both.  You need to correct such protons to have the right names.
	You could either do this by hand with an editor or, if you don't need the specific protonation state of your starting structure, by deleting all the hydrogens in Chimera ("del H") and then adding them back ("addh").  This assumes that your heavy atom names are standard.  If they are not, those would need to be fixed by hand.

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu


On Mar 17, 2015, at 10:39 PM, Mahendra B Thapa <thapamb at mail.uc.edu> wrote:

> 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 mailing list
> Chimera-users at cgl.ucsf.edu
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