Re: [AMBER] MMPBSA error

From: Ray Luo <rluo.uci.edu>
Date: Wed, 11 Oct 2017 07:58:55 -0700

Great!

Ray
--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical Physics, Biomedical Engineering, and Chemical Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Wed, Oct 11, 2017 at 3:37 AM, sangita kachhap <nckachap.cyf-kr.edu.pl> wrote:
> Thanks for the reply, Ray.
> My problem is solved now. It was not the problem with AMBER but there was
> some MPI problem in the computing system.
>
> Thanks
>
> On Tue, Oct 10, 2017 at 8:50 AM, Ray Luo <rluo.uci.edu> wrote:
>
>> Sangita,
>>
>> My suggestion is to use the sander option and keep the output files.
>> After the new run please email the mdout files to us. So far it's hard
>> to see what's going on with your runs ...
>>
>> All the best,
>> Ray
>> --
>> Ray Luo, Ph.D.
>> Professor of Structural Biology/Biochemistry/Biophysics,
>> Chemical Physics, Biomedical Engineering, and Chemical Engineering
>> Department of Molecular Biology and Biochemistry
>> University of California, Irvine, CA 92697-3900
>>
>>
>> On Mon, Oct 9, 2017 at 7:27 AM, sangita kachhap <nckachap.cyf-kr.edu.pl>
>> wrote:
>> > Dear AMBER Developer
>> >
>> > I am doing free energy calculation for protein-ligand complex using
>> > amber16. I am getting all the energy values by GB calculation but not by
>> PB
>> > calculation.
>> >
>> > BOND                         0.0000                0.0000
>> > 0.0000
>> > ANGLE                        0.0000                0.0000
>> > 0.0000
>> > DIHED                        -0.0000                0.0001
>> > 0.0000
>> > VDWAALS                -21.7043                3.5652              0.4603
>> > EEL                          -67.5611               13.6737
>> > 1.7653
>> > 1-4 VDW                      0.0000                0.0000
>> > 0.0000
>> > 1-4 EEL                       0.0000                0.0000
>> > 0.0000
>> > EPB                              nan                    nan
>> > nan
>> > ENPOLAR                  -0.5965                1.5886
>> 0.2051
>> > EDISPER                       nan                   nan
>>  nan
>> >
>> > DELTA G gas             -89.2654               12.8027
>> 1.6528
>> > DELTA G solv                  nan                   nan
>>  nan
>> >
>> > DELTA TOTAL                  nan                   nan
>>  nan
>> >
>> > Herewith I am attaching mmpbsa output file.
>> >
>> > I also checked the water and ion striped trajectory of complex with
>> prmtop
>> > file (which I have used for MMPBSA calculation) in VMD, both files are
>> > compatible.
>> >
>> >
>> > Please suggest me how to solve it.
>> >
>> > Thanks
>> >
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>> >
>>
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Received on Wed Oct 11 2017 - 08:30:02 PDT
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