AMBER Archive (2002)

Subject: Re: DNA Tutorial Script

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Wed Sep 04 2002 - 22:29:23 CDT

Dear Joel,

I had a look into the first two sander calculations, i.e. the ones with
min.belly.in and md.belly.in in Run.equil.

You have to make the following changes:
1. In atA.coords, add as the last line in the file the box coordinates:
"61.317974 41.857475 41.857475 90.0000000 90.0000000 90.0000000"

2. In min.belly.in, add "ntp = 1," to the &cntrl namelist.

3. In md.belly.in, remove "ndfmin = 0, init = 3, tauts = 0.2, nrun
= 1" from the name list and add "nmropt = 1".

This equilibration part still "suffers" from going from amber6 to
amber7, I'm currently testing the following simulations in Run.equil.
Thank you for reporting the problem.

Best regards

Holger

> When running the Run.equil script found in the DNA tutorial
> <http://sigyn.compchem.ucsf.edu/amber/tutorial/polyA-polyT/equilibration.html>,
> I get the following error message.
>
> ----------------------
> $ Run.equil sander
> Arithmetic Exception
> FAILED. Sorry bud.
> ----------------------
>
> I've downloaded all the input files. What's going on?
>
> -Joel 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++