Dear experts,
I suddenly found that a pdb file which I use ambpdb script to generate
looks like this.
ATOM 10377 CA NMG 684 52.546 49.086 64.805 0.00 0.00 C
ATOM 10378 1HA NMG 684 51.564 49.216 64.350 0.00 0.00 1
ATOM 10379 2HA NMG 684 52.607 48.601 65.779 0.00 0.00 2
ATOM 10380 C NMG 684 53.245 48.102 63.859 0.00 0.00 C
where NMG is the name of a non-standard residue. Note that the elements in
red color. Normally the numbers 1 and 2 should be element H. Does this
affect the MD as well as the MM_GBSA free energy results? The error
happened in the ligand structure.
Look forward to your reply.
Sincerely yours,
Jack
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 25 2014 - 02:00:02 PDT
