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.
I checked the original mol2 file for the non-standard residue. The element
symbol are right however, as shown below:
2 CA -0.128891 0.758463 -1.045314 C 1 NMG
-0.0933 ****
3 1HA -0.061778 0.090460 -1.890037 *H * 1 NMG
0.0767 ****
4 2HA -0.141346 1.779741 -1.397777 *H* 1 NMG
0.0767 ****
5 C -1.419790 0.528572 -0.264945 C 1 NMG
0.5948 ****
So now I am confused. I really look forward to your reply.
Sincerely yours,
C.Q.
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Received on Fri Jul 25 2014 - 02:00:03 PDT
