Hi there,
I have problem once again with ligand in my PDB file. It is a heme group. I extracted the coordinates for heme group from 1CX2 PDB structure into a file and ran the the "reduce" command. It added the hydrogens. But this time I am having problem using "anechamber". Here is the error message:
Running: /share/apps/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 303; net charge: 0
INFO: Number of electrons is odd: 303
Please check the total charge (-nc flag) and spin multiplicity (-m flag)
Running: /share/apps/amber11/bin/sqm -O -i sqm.in -o sqm.out
It seems that I can generate mol2 file if I do not use the -c flag.
I have attached the sqm.out, and the pdb and mol2 coordinate files.
I will appreciate your kind help.
Best regards,
Siavoush
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- application/octet-stream attachment: sqm.out
- application/octet-stream attachment: t5.pdb
- application/octet-stream attachment: t5.mol2
Received on Wed Sep 23 2020 - 08:30:02 PDT
