AMBER Archive (2006)

Subject: Re: AMBER: problem with amber 9 and igb=5

From: John Mongan (jmongan_at_mccammon.ucsd.edu)
Date: Wed Jun 07 2006 - 21:04:59 CDT

Can you be more specific about "hangs"? Does the program exit or stay
running? Do you continue to see output to the mdout file? If you run
top, is it using the maximum processor that it can, or is it
stopped/blocked?

Also, what compiler and platform are you using?

This seems very curious because igb=7 uses all of the code used by igb=5
(plus a little more for the neck correction).

John

M. Scott Shell wrote:
> Hello,
>
> I am having a problem using amber 9 with igb=5 to minimize a short
> peptide sequence in sander. For some reason, sander often hangs during
> the minimization procedure, although sometimes it seems to work just
> fine. Using the same input files amber 8 always works smoothly without
> hanging, however. Amber 9 also seems to work smoothly with igb=7 and
> igb=1. I am wondering if this is a bug in amber 9 or simply a hiccup in
> my input files or something specific to my system. The inputs are below
> (the restraints.txt file mentioned is empty for this particular run).
> Any thoughts?
>
> Many thanks,
>
> M. Scott Shell
> Postdoctoral scholar, Dill group
> Department of Pharmaceutical Chemistry
> University of California San Francisco
>
>
> ---TLEAP INPUT (seems to work fine)---
> source leaprc.ff96
> set default PBradii mbondi2
> seq = {ACE ASP LEU GLY VAL LYS GLU LYS LEU ILE GLU LYS ALA NME}
> sys = loadPdbUsingSeq init04.pdb seq
> check sys
> saveAmberParm sys prmtop.parm7 tleapout.crd
> savepdb sys tleapout.pdb
> quit
>
> ---SANDER INPUT---
> Minimization - steepest descent followed by conj grad
> &cntrl
> imin=1, maxcyc=1050, ncyc=1000,
> igb = 5, gbsa = 1,
> cut = 16.0,
> ntc = 1, ntf = 1, tol = 1.0d-8,
> ntb = 0, iwrap = 0,
> ntpr=100, ntwr=1000,
> nmropt = 1,
> ntr = 0,
> &end
> &wt type='REST', istep1=0, istep2=100, value1=1.0,
> value2=1.0, &end
> &wt type='END' &end
> DISANG=restraints.txt
>
> END
> END
>
> ---COMMAND LINE---
> sander -O -i minin.txt -o minout.txt -p prmtop.parm7 -c tleapout.crd -r
> minout.crd -e minene.txt -inf mininfo.txt
>
>
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