Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 30 Sep 2013 10:07:20 -0600

Hi,

On Mon, Sep 30, 2013 at 7:18 AM, Ƚͦ <rantingjing0445019.gmail.com> wrote:
> [cli_0]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> [cli_2]: aborting job:

Where any output files produced (mdout, the '-o' file in particular)?
Were there any error messages in those files? Also, what version of
Amber are you using and what bugfixes have been applied?

-Dan

> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
> rank 0 in job 230 localhost_39799 caused collective abort of all ranks
> exit status of rank 0: return code 1
>>>
> I used 4 cpus to run sander.MPI
>
>
> On Mon, Sep 30, 2013 at 8:01 PM, David A Case <case.biomaps.rutgers.edu>wrote:
>
>> On Mon, Sep 30, 2013, Ƚͦ wrote:
>>
>> > I read the tutorial that's "Thermodynamic Integration using soft
>> core
>> > potentials
>>
>> > I want to modeling the water contribution to the ligand-binding affinity
>> by
>> > the double decoupling method.
>>
>> It's not clear what you mean by the "water contribution to the ligand
>> binding
>> affinity". A "standard" simulation of the ligand binding free energy will
>> automatically include the effects of the solvent.
>>
>> > I wonder if the icfe parameter should be set from minimization
>> > mdin to equilibrium mdin
>>
>> You would ordinarily use the same icfe value at all steps. Note that
>> minimization is often not needed.
>>
>> > if the water should be constraint at the
>> > binding site by a constraint force as described in the literature
>>
>> You would ordinarily not constraint solvent molecules. But note that it
>> may
>> take a long time to equilibrate if there are trapped waters.
>>
>> > As well, I cannot use the pmemd method to run Thermodynamic Integration
>>
>> This is correct; the next release of pmemd will have this feature.
>>
>> > My command is "sander -ng 2 -groupfiles Mygroupfiles"
>> > the erro is "mdfil: Error unknown flag: -ng" but the recommended
>> > parameters include the -ng flag. I used amber10.
>>
>> You must use sander.MPI (not sander), and the corresponding mpirun command
>> to
>> carry out thermodynamic integration calculations.
>>
>> Since you seem to be very new to this, be sure to get familiar with small
>> and
>> "easy" transformations before attempting something difficult.
>>
>> ...good luck...dac
>>
>>
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>>
>
>
>
> --
> PhD Ting Ran
>
> CPU(CHINA PHARMACEUTICAL UNIVERSITY)
> Molecular-Design & Drug-Discovery Lab
> Laboratory Building A212
> 639 Longmian Avenue
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> P.R.China
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-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Sep 30 2013 - 09:30:03 PDT
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