By the way, the MD ran normally and reported no errors.
On Fri, Jul 25, 2014 at 4:52 PM, Changqing Yan <ycqchemical.gmail.com>
wrote:
> 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 - 02:30:02 PDT
