[AMBER] Heme parameters

From: Siavoush Dastmalchi <dastmalchi.s.tbzmed.ac.ir>
Date: Wed, 23 Sep 2020 18:30:19 +0330

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,

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Received on Wed Sep 23 2020 - 08:30:02 PDT
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