[Chimera-users] PROBLEM IN ENERGY MINIMIZATION
meng at cgl.ucsf.edu
Tue Oct 1 14:43:56 PDT 2019
Antechamber is not our code, but as far as I can tell, it looks like it cannot correctly identify atom types for this ligand molecule, which prevents Gasteiger charge calculation. Although it does not prevent AM1-BCC charge calculation, and that appears to give fairly reasonable charges,the atoms themselves are only assigned type “DU” (which usually means “dummy”). I’m guessing that this dummy atom type doesn’t have parameters (VDW radius, bond lengths and angles, etc.), and that is why the minimization messes up the structure. I don’t know what exactly is causing the problem, sorry.
In Chimera you could try minimization with the ligand atoms frozen so that they cannot move at all, but that may defeat the purpose of minimization.
I don’t have any solution, sorry. Antechamber/GAFF are meant to handle most small organic molecules, but some just cause problems.
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
> 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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