Query on the force field for energy minimization
Dear Sir I would be grateful if you kindly let me know what force field is used by Chimera to optimize the geometry of a small organic molecule (not peptide) if I minimize the structure using the parameters as shared in the attached file. Thank you Kind regards *Prabuddha Bhattacharya * [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> 13/01/24, 15:02:51
This information is in the Help page for this tool. You can click the Help button on the "Minimize Structure" dialog or see the copy on our website here: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html> Specifically, see the section "Force Field Parameters" and "nonstandard residues" <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#nonstandard> Short answer is that is uses GAFF (see details in link above) with the type of charges you chose in the dialog, from your image Gasteiger. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 13, 2024, at 1:33 AM, Prabuddha Bhattacharya via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Sir
I would be grateful if you kindly let me know what force field is used by Chimera to optimize the geometry of a small organic molecule (not peptide) if I minimize the structure using the parameters as shared in the attached file.
Thank you
Kind regards
Prabuddha Bhattacharya
Thank you so much sir for your response. It was very helpful. Kind regards On Sun, 14 Jan 2024, 21:56 Elaine Meng, <meng@cgl.ucsf.edu> wrote:
This information is in the Help page for this tool.
You can click the Help button on the "Minimize Structure" dialog or see the copy on our website here: < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize...
Specifically, see the section "Force Field Parameters" and "nonstandard residues" < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize...
Short answer is that is uses GAFF (see details in link above) with the type of charges you chose in the dialog, from your image Gasteiger.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 13, 2024, at 1:33 AM, Prabuddha Bhattacharya via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Dear Sir
I would be grateful if you kindly let me know what force field is used by Chimera to optimize the geometry of a small organic molecule (not peptide) if I minimize the structure using the parameters as shared in the attached file.
Thank you
Kind regards
Prabuddha Bhattacharya
participants (2)
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Elaine Meng -
Prabuddha Bhattacharya