[Chimera-users] PROBLEM IN ENERGY MINIMIZATION
pett at cgl.ucsf.edu
Wed Oct 2 17:26:12 PDT 2019
If you were using the same input file with the blank residue name, I have no idea how it would have worked before — sorry.
> On Oct 1, 2019, at 10:10 PM, Prabuddha Bhattacharya <b.prabuddha3 at gmail.com> wrote:
> Thank you Sir.. Your suggestion worked perfectly.. There was no problem in minimizing the structure once I assigned a residue name as per your suggestion.
> However I had one query, I was able to minimize the same structure earlier without any intermediate step.. But recently this problem of ANTECHAMBER failure popped up. How can I justify this computational anomaly? Please note that neither have I changed my computational system, nor have I uninstalled/reinstalled UCSF Chimera in this period. How could it be so that a structure that could be minimized earlier was creating trouble to minimize recently (until sorted out as per your suggestion).
> I will be highly grateful if you can kindly give me some probable reason to justify this anomaly,
> Thank you again for your sincere help and prompt support,
> With best regards,
> Prabuddha Bhattacharya
> Assistant Professor
> Adamas University
> Kolkata 700126
> On Wed, Oct 2, 2019 at 3:13 AM Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
> Hi Prabuddha,
> 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.
> Eric Pettersen
> UCSF Computer Graphics Lab
>> On Oct 1, 2019, at 11:43 AM, Prabuddha Bhattacharya <b.prabuddha3 at gmail.com <mailto: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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