Hi Eric, yes, the command fixes the problem. The CYMs are present due to the presence of five zinc fingers. Following is the output: setattr [5] :CYM r name CYS Assigning name attribute to 15 items coulombic [6] protein Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for rep.c3.mgs_charged.pdb_ SES surface #1.1: minimum, -22.87, mean -0.35, maximum 60.32 If possible, another question. The protein has two magnesium ions coordinated by two Asp and two Glu. After the surface has been drawn only one Mg is outside whereas the other one is inside the surface. In the images what can be seen. Any suggestions about the reasons why it does so? Thanks. Saverio Il 19.10.2024 02:44 Eric Pettersen ha scritto:
If you run this command before running colombic, does it fix the problem?
setattr :CYM r name CYS
--Eric
On Oct 12, 2024, at 7:13 AM, saverio via ChimeraX-users wrote: Hi, I have six representative frames, in pdb format , of six clusters evaluated with cpptraj of a trajectory . For three representative frames the command "coulombic protein" the surface is produced without any problem whereas for the remaining three I receive errors similar to the following text: coulombic protein Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue CYM (net charge -1) with am1-bcc method Running ANTECHAMBER command: /usr/lib/ucsf-chimerax/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /tmp/tmp76d1_frw/ante.in.mol2 -fi mol2 -o /tmp/tmp76d1_frw/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n (CYM) (CYM) Welcome to antechamber 20.0: molecular input file processor. (CYM) (CYM) Info: Finished reading file (/tmp/tmp76d1_frw/ante.in.mol2); atoms read (22), bonds read (21). (CYM) Info: Determining atomic numbers from atomic symbols which are case sensitive. (CYM) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (CYM) (CYM) (CYM) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (CYM) Info: Total number of electrons: 94; net charge: -1 (CYM) (CYM) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out (CYM) (CYM) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-chimerax/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1 (CYM) (CYM) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC (CYM) Charges for residue CYM determined Assigning partial charges to residue CYM (net charge -1) with am1-bcc method CYM: number of electrons (92) + formal charge (-1) is odd; cannot compute charges for radical species using AM1-BCC method Any suggestions to solve this problem? Thanks. Saverio _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu [2] To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu [3] Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ [4]
