AMBER Archive (2003)

Subject: Re: Problem with LES topology file

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue Jun 17 2003 - 17:42:07 CDT

what version of amber are you using?
that analysis program doesn't read the new prmtop
format files from amber7. we'll have to update
it, in the meantime you can use the new2oldprm
utility in amber to write an old format prmtop.
the analysis program will read that.
carlos

===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

----- Original Message -----
From: "Courtney Stanton" <cstanton78_at_hotmail.com>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Tuesday, June 17, 2003 6:28 PM
Subject: Problem with LES topology file

> Hello all,
>
> I am trying to use the undocumented analysis program from the MOIL-View
page
> to average the copies from a LES simulation into a single-copy file.
> However,
> whenever I read the topology file created by addles, I get the following
> error:
>
> AMBER 4.1 style LES not detected
> Error reading initial variable list in parm file.
> Problem reading parameter file
>
> I ran the LES simulation for 1ns with no apparent problem. Here is my
addles
> input file when I created the LES topology file:
>
> file rprm name=(file.top) read
> file rcvb name=(file.rst) read
> file wprm name=(file_les.top) wovr
> file wcrd name=(file_les.crd) wovr
> action
> ~
> omas
> ~
> spac numc=5 pick #mon 206 211 done
> *EOD
>
> Any helpful suggestions would be greatly appreciated!
> Thank you in advance!
> Courtney
>
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