Hi Obdulia,
The pbmd simulation in the current amber8 release does not run on
partially solvated solute, i.e. the solute has to be fully solvated in a
water droplet (cap). If this is not the reason for the failure, how
about you email me your prmtop and rst files for me to reproduce your
problem?
We expect an update of pbmd functionality in the summer that will take
care of paritally solvated cases.
All the best,
Ray
Obdulia Rabal wrote:
>Dear all.
>
>When running a molecular simulation with igb = 10 (and default pb
>parameters ) the following message appears:
>
> PB warning in pb_miccg():CG maxitn exceeded!!!!
>
>My input looks like:
>
> &cntrl
> imin=0, irest=0, nmropt=1,
> ntx=1, ntpr=100, ntwx=500, ntwv=500, ntwe=500,
> ntf=2, ntc=2, tol=0.000001,
> ntb=0, igb=10, cut=300.0, scnb=2, scee=1.2,
> ibelly=0, ntr=0,
> nstlim=25000, ntt=1, tautp=1,
> dt=0.002,
> &end
> &pb
> npbverb=0,
> &end
> &wt
> type='TEMP0', istep1=0, istep2=25000,
> value1=0, value2=300.0,
> &end
> &wt
> type='END'
> &end
>
>and I have partially solvated around a residue ( I doubt if that's possible,
>as it stands in
>manual page 139).
>
>Any help will be appreciated.
>Thanks in advance.
>
>Obdulia Rabal
>
>
>
>
>
>
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>.
>
>
>
--
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528 Lab: (949)824-9562
Fax: (949)824-8551 e-mail: rluo.uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
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Received on Tue May 18 2004 - 19:53:00 PDT
