Hi The problem is resolved by changing the name of OC1 to O and OC2 to OXT. Although the names are produced by AMBER99SB forcefield. Thank you very much for your help ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, January 30, 2025 6:10 PM To: fateme haghighi <fateme.haghighi@outlook.fr> Cc: Eric Pettersen via Chimera-users <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Charges of 0.0 were assigned to the unknown atoms As you can see from the Reply Log messages, it is much better now, but you still have two weird atom names in one residue:
On Jan 30, 2025, at 12:53 AM, fateme haghighi via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Non-standard atom names: ALA OC2 (ALA 480 OC2) ALA OC1 (ALA 480 OC1) Total charge for #0: -9.432 The following residues had non-integral charges: ALA 480 0.5679
We have no idea what those atoms are, so we don't know what names they are supposed to have. Alanine does not have "OC1" and "OC2" atoms. You need to look at that residue and figure out what they are and whether you need them, and whether the residue is really an alanine or something else. If it is an alanine, you need to use PDB standard atom names for alanines. Alternatively, if that one residue with non-integral charge is not close to the ligand binding site for docking, this charge discrepancy may not be very important and you might choose to ignore it. 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