Setting partial charges to a protein gives same charges in both Gasteiger and AM1-BCC methods. Is that corrects?
Dear colleagues, calculation of partial charges in Chimera looks to work improperly in my hands. After addcharge or dokprep procedures, independent on method used (am1-bcc or Gasteiger), mol2 files are just the same: @<TRIPOS>MOLECULE .... PROTEIN AMBER ff14SB @<TRIPOS>ATOM 1 N -76.5030 6.5380 -16.5070 N.4 1 ARG 0.1305 2 CA -75.2450 7.2900 -16.2110 C.3 1 ARG -0.0223 .... The problem persist in both Chimera 1.17.3 and ChimeraX. The latter gives even "NO_CHARGES" comment in both (am1-bcc and Gasteiger) cases: @<TRIPOS>MOLECULE .... PROTEIN NO_CHARGES @<TRIPOS>ATOM 1 N -76.5030 6.5380 -16.5070 N.4 1 ARG 0.1305 2 CA -75.2450 7.2900 -16.2110 C.3 1 ARG -0.0223 .... I am not an expert in molecular modeling, sorry. But I think that I am doing something wrong. Could you please help me with setting charges properly? Thank you in advance! PS. I am a newbie here. Please don't hurt me too much. Yours sincerely, Al.
Hello, The protein charges for standard amino acids are just a lookup table from the specified force field, apparently AMBER ff 14SB. Maybe the NO_CHARGES line from ChimeraX is just a small bug that doesn't matter much since the charges are there. The calculation choice am1-bcc or Gasteiger is only for the nonstandard residues like some ligands or modified amino acids. So choosing one or the other would not have any effect on standard amino acids in proteins, only on those nonstandard residues. 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 Mar 2, 2025, at 5:04 AM, teralexei--- via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear colleagues, calculation of partial charges in Chimera looks to work improperly in my hands. After addcharge or dokprep procedures, independent on method used (am1-bcc or Gasteiger), mol2 files are just the same:
@<TRIPOS>MOLECULE .... PROTEIN AMBER ff14SB @<TRIPOS>ATOM 1 N -76.5030 6.5380 -16.5070 N.4 1 ARG 0.1305 2 CA -75.2450 7.2900 -16.2110 C.3 1 ARG -0.0223 ....
The problem persist in both Chimera 1.17.3 and ChimeraX. The latter gives even "NO_CHARGES" comment in both (am1-bcc and Gasteiger) cases:
@<TRIPOS>MOLECULE .... PROTEIN NO_CHARGES @<TRIPOS>ATOM 1 N -76.5030 6.5380 -16.5070 N.4 1 ARG 0.1305 2 CA -75.2450 7.2900 -16.2110 C.3 1 ARG -0.0223 ....
I am not an expert in molecular modeling, sorry. But I think that I am doing something wrong. Could you please help me with setting charges properly? Thank you in advance!
PS. I am a newbie here. Please don't hurt me too much.
Yours sincerely, Al. _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
participants (2)
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Elaine Meng -
teralexei＠proton.me