AMBER Archive (2003)

Subject: Re: tleap in large systems

From: GUILLERMINA L ESTIU (gle10_at_psu.edu)
Date: Thu Mar 27 2003 - 14:57:21 CST

Yes, I was just looking at that.
It is not necessary to change also the
      PARAMETER (RMAX = 9999.99D0)
      PARAMETER (RMIN = -999.99D0)
in dynlib.f ?

On Thu, 27 Mar 2003 12:43:01, "David A. Case" wrote:

> On Wed, Mar 26, 2003, GUILLERMINA L ESTIU wrote:
> >
> > I am using amber6. I am dealing with a large system that has 47000 residues
> > (water box included)
> > When using tleap the top and crd files are not built properly.
> > Tleap does not complain, but when trying to use them in the minimization
> > (sander) I got a message FATAL: NATOM mismatch in coord and topology files
>
> Amber 6 was not set up very well to handle systems with more than 100000
> atoms, even though tleap does not complain.
>
> The easiest thing to do is to upgrade to amber 7. Alternatively, you can
> modify the section (in routine getcor) that reads the number of atoms. It
> probably needs to use an I6 rather than an I5 format to correctly read the
> input files you have.
>
> ..hope this helps...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================
>
>
>

Dr Guillermina Estiu
Chemistry Department
Pennsylvania State University
PA 16802