AMBER Archive (2005)

Subject: Re: AMBER: nmropt =1 AND ntr=1 in pmemd

From: Furse, Kristina Elisabet (kristina.e.furse_at_vanderbilt.edu)
Date: Fri Jun 17 2005 - 14:16:13 CDT


Hi Robert-

We have indeed been down this road before--I think I sent you a test case.
Here's our thread from the mailing list archive if that helps:

http://structbio.vanderbilt.edu/archives/amber-archive/2004/0323.php

I'll search my email to see if I can find the resolution, since I can't recall
what happened!

Kristina

Quoting Robert Duke <rduke_at_email.unc.edu>:

> Cristoph -
> Which version of pmemd? Have you tried the inputs with sander 7 or sander
> 8, just a short run to see if it works? If you would like me to take a more
>
> detailed look, please put the prmtop/inpcrd/mdin and additional redirections
>
> in a tarball and mail it directly to me (at rduke_at_email.unc.edu) and I will
> look at it, and if there is a deficiency in pmemd, patch it and send you the
>
> patch. The story on these more complicated input modes is that starting
> from the first pmemd releases, I made the namelist reading code more
> reliable by rewinding after every namelist read, thus making namelist
> reading position independent. Now, I know that these two types of
> restraints work alone, but I am not sure whether I have ever been asked if
> they work together. Anyway, I will be glad to look at it, but because we
> don't have this sort of test case, it would be helpful if you send your
> input.
> Regards - Bob Duke
>
> ----- Original Message -----
> From: "Christoph Brockmann" <brockmann_at_fmp-berlin.de>
> To: <amber_at_scripps.edu>
> Sent: Tuesday, June 14, 2005 5:33 AM
> Subject: AMBER: nmropt =1 AND ntr=1 in pmemd
>
>
> > Dear mailing list,
> >
> > I try to run amber8 pmemd with both nmr AND positional restraints.
> > However, it seems impossible to get pmemd to read both types of
> > restraints.
> >
> > If I give the group information after the redirects (in a sander7 fashion)
> >
> > %<
> >
> >
> > LISTIN=SOLVRUN1_c.restraints
> >
> >
> >
> > LISTOUT=SOLVRUN1_c.violations
> >
> >
> > DISANG=test.rst
> > Positional
> > restraints
> >
> > 100
> >
> >
> >
> > FIND
> >
> >
> > SD * *
> > *
> >
> > SEARCH
> >
> >
> > RES 1
> > 10
> >
> > END
> >
> >
> >
> > END
> >
> >
> >
> > STOP
> >
> >
> > %<
> >
> > I get:
> >
> > %<
> > 5. REFERENCE ATOM COORDINATES
> >
> >
> >
> >
> > ----- READING GROUP 1; TITLE:
> > LISTIN=SOLVRUN1_c.restraints
> >
> >
> > rfree: Error decoding variable 1 3 from:
> > LISTOUT=SOLVRUN1_c.violations
> > %<
> >
> > If I give the Group BEFORE the redirects the group information is read
> > and understood but the redirects themselves are not found anymore
> > resulting in absolutely NO nmr-restraints. Is there a way to solve this
> > problem?
> >
> > Christoph
> >
> >
> >
> > -----------------------------------------------------------------------
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> >
>
>
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-----------------------------------------------------------------
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
Email: kristina.e.furse_at_Vanderbilt.Edu
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