Hi,
Remove the NTX from your mmpbsa.pl input
On Tue, May 18, 2010 at 6:11 PM, Seungyeul Yoo <Seungyeul.Yoo.mssm.edu>wrote:
> Dear Amber Users,
>
> I am using mm_pbsa.pl version now and have a error message during
> normal mode analysis.
>
> After I generated snapshots from my MD simulations (Results are
> stable), I could calculate PB and GB solvation energy with successful
> energy decomposition.
>
> However, when I tried to calculate entropy terms, nmode input files
> indicated "ntx = 0".
>
> Since my coordinate files are formated, calculation stops very
> beginning.
>
> Even when I set ntx = 1 in mm_pbsa input file as following, nmode
> input files which are automatically generated by mm_pbsa.pl still have
> ntx = 0.
>
> .NM
> #
> # Parameters for sander/nmode calculation (this section is only
> relevant if NM = 1 above)
> #
> # The following parameters are passed to sander (for minimization)
> and nmode
> # (for entropy calculation using gasphase statistical mechanics).
> # For further details see documentation.
> #
> # DIELC - (Distance-dependent) dielectric constant
> # MAXCYC - Maximum number of cycles of minimization.
> # DRMS - Convergence criterion for the energy gradient.
> #
> DIELC 4
> MAXCYC 1000
> DRMS 0.1
> NTX 1
> #
>
> Isn't default value of ntx for normal mode 1? I'm wondering if there
> is a way I can make nmode input files have ntx as 1.
>
> Thanks in advance,
>
> Best regards,
>
> Seungyeul Yoo, Ph.D Candidate
> Department of Structural and Chemical Biology
> Mount Sinai School of Medicine
> Box 1677, 1425 Madison Avenue, New York, NY 10029
> East Building, 16th floor, Room 16-34A
> New York, NY 10029
> +1 (212) 6595477
>
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>
--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Tue May 18 2010 - 16:00:03 PDT
