Dear Ray,
Thanks for the update. I reinstalled amber 14 yesterday and it
automatically applied the patches. However, mmpbsa still didn't like inp=2
with radiopt=0.
The irony is I had 2 years old installation of amber 12 (probably with
ambertools 1.3) which worked with my current system with inp =2.
I look forward to hear from you regarding patches for amber 14.
Many thanks,
Neha
On 04/04/2015 1:28 am, "Ray Luo, Ph.D." <ray.luo.uci.edu> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Apr 03 2015 - 20:00:02 PDT
