Re: [AMBER] MMPBSA issues with ff12SB

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Fri, 3 Apr 2015 10:28:20 -0700

Hi Neha,

If you are using the latest AmberTools, radiopt=0 should work with
both inp=2 and inp=1. Have you patched all updates? I remember there
were some inconsistencies between the master source tree and the
released version last year. The updates should have brought the
released version up to date. Let me know if you still cannot run it
with the updated Amber14.

All the best,
Ray

--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Fri, Apr 3, 2015 at 8:34 AM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> Dear List,
>
> I have used ff12SB forcefield and I am trying to do MM-PBSA calculation.
>
> I tried changing atom types such from CI to C using parmed.py as per the
> this post on the mailing list
> http://archive.ambermd.org/201208/0074.html
>
> Once I got rid of this atomtype, MMPBSA complained about CB. I saw this
> mailing list by Ray Luo
> http://archive.ambermd.org/201409/0222.html
>
> I am using AMBER14 and I was wondering if any progress has been made in
> this regards? I tried radiopt=0 but it didn't help with inp=2.
>
> Any help is appreciated.
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Curtin Research Fellow,
> School of Biomedical Sciences,
> Curtin University,
> Perth GPO U1987
> Australia
> LinkedIn
> Research Gate
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Received on Fri Apr 03 2015 - 10:30:02 PDT