Re: [AMBER] MMPBSA issues with ff12SB

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Fri, 3 Apr 2015 22:00:53 -0700

Neha,

Can you email me your input file? Are you using the python script or
the perl script?

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 7:43 PM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> 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
>> > _______________________________________________
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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Fri Apr 03 2015 - 22:30:02 PDT
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