(unknown charset) [AMBER] Re: Fw:SOS for mmpbsa

From: (unknown charset) Ray Luo <ray.luo.uci.edu>
Date: Wed, 10 Mar 2010 10:17:07 -0800

//Hi Yangsy,
> I am trying to do nmode calculation of mm_pbsa method using amber10
> and have maken maxcyc=500000 drms=0.0001 in input file, But I got the
> following error message: "Warning: Not all of your snapshots minimized
> within tolerable limits for nmode", but final NSTEP in
> _MMPBSA_nmode_minlig.mdouts is only 14850 less than 20000 . Moreover,
> I find following message in _MMPBSA_ligand_nm.out file:
> "Root-mean-square gradient of input coords is 0.29789907
> This is greater than the requested maximum: 1.E-05 "
> the messages above yet exist in _MMPBSA_complex_nm.out and
> in_MMPBSA_respect_nm.out
> So, could you help me to check the problem and give me some instructions?
> I'm looking forward to your reply.
> yangsy
I'm forwarding your question to the Amber mailing list ... the question
and answers will certainly benefit many other Amber users.

So far there is too little information in your email. Do you have a very
large system? Do all snapshots fail to converge? Can we take a look of
your input file?

All the best,

Ray Luo, Ph.D.
Associate Professor in Computational
Biochemistry and Molecular Biophysics
Dept of Molecular Biology and Biochemistry 
Dept of Biomedical Engineering
University of California, Irvine, CA 92697-3900
Email: rluo.uci.edu Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/rayl/
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Received on Wed Mar 10 2010 - 10:30:02 PST
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