AMBER Archive (2008)

Subject: Re: AMBER: GBSA SA calculation

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed May 07 2008 - 14:05:44 CDT

try setting ntwx=1

On Wed, May 7, 2008 at 2:32 PM, Titus, Jamie (bairdje)
<BAIRDJE_at_ucmail.uc.edu> wrote:
>
>
>
>
> Hello all,
>
> I am currently trying to extract SA terms from a trajectory which I have
> stripped of H2O and ions, recreated the proper water/ion free prmtop, and
> used the following input file and command to run the calculation:
>
> surface.in - Calculate solvent accessible surface area
> &cntrl
> imin = 5,
> gbsa = 2,
> igb = 1,
> ntb = 0,
> surften = 1,
> cut = 99,
> /
>
> sander -O -i surface.in -p waterandionfree.prmtop -x
> trajectorystrippedofH2Oandions.crd -c waterionfreeoriginalcrd.crd -o
> surface.out
>
> I have tried this procedure with several different trajectories of
> different systems, and each time I am getting the following error:
>
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
> POST-PROCESSING OF TRAJECTORY ENERGIES
> Error in trajectory file
> error in trajene()
>
> Not sure what the problem is - didn't see it in the archive anywhere.
> Using serial installation of Amber9 on a Linux AMD Opteron Dualcore.
>
> Jamie Baird-Titus
> Post-Doctoral Fellow
> Laboratory of Professor Mark Rance
> Department of Molecular Genetics, Biochemistry, and Microbiology
> University of Cincinnati College of Medicine
> Rm. 3109 Medical Sciences Bldg.,
> 231 Albert Sabin Way, Cincinnati, OH 45267
> phone:(513)558-2938
> email:bairdje_at_ucmail.uc.edu
> website: http://jamiebairdtitus.googlepages.com
>
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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