[Chimera-users] PROBLEM IN ENERGY MINIMIZATION
pett at cgl.ucsf.edu
Tue Oct 1 14:43:45 PDT 2019
The underlying AmberTools programs that Chimera is calling to perform the atom typing and minimization don’t work properly if the residue name is blank. If your sulfonamide is open as model #0, do this command (Favorites→Command Line) before minimizing in order to assign a residue name of “UNL”:
setattr r type UNL #0
Then both Gasteiger and AM1-BCC minimizations will work.
UCSF Computer Graphics Lab
> On Oct 1, 2019, at 11:43 AM, Prabuddha Bhattacharya <b.prabuddha3 at gmail.com> wrote:
> Dear Chimera,
> I have been facing a problem recently while using UCSF Chimera. After opening the structure of ligands in the chimera window as .pdb file, when ever I am trying to minimize the energy (Tools-->Structure Editing-->Minimize Structure) of that ligand in (which is in .pdb form), I am getting the following error message: "Failure running ANTECHAMBER for residue". I am using "AMBER ff14SB" (for standard residues) and "Gasteiger" (for other non-standard residues).
> Upon trying out with "AM1-BCC" (for other non-standard residues), I am getting an altered compound so that cannot be perhaps tried.
> Kindly find attached the .pdb files for the ligands I am trying to minimize the energy, and a word file containing the screen shots of the step-by-step messages leading to the error message that I am getting.
> I will be highly grateful if you can help me in sorting out the problem.
> Thanks in advance,
> Best Regards,
> Prabuddha Bhattacharya
> Assistant Professor
> Adamas University
> Kolkata 700126
> <sulfonamide-pdb.pdb><energy minimization problem.docx><vb.pdb>_______________________________________________
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