AMBER Archive (2006)

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

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Wed Jun 07 2006 - 21:02:34 CDT

Scott,
I don't see any obvious problems but have you tried it without the
weight change?

also unless this is just some test system I would really avoid using
ff96 as it is
quite bad, not just the (strong) beta bias but your glycine will almost
certainly be
very misbehaved. I would not use this combination and would have very
serious reservations about any article that I read where it was used.
We've also shown that igb1 and igb5 have a very strong alpha helical
bias, and
while the combination of gb and ff96 might sometimes seem to give
secondary structure
propensities in line with experiment it would be for all the wrong reasons.
just my opinion... I really want people to stop using this parameter
set. Even the
Kollman lab where it was developed abandonded it very quickly.
Carlos

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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