AMBER Archive (2005)

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

From: Robert Duke (rduke_at_email.unc.edu)
Date: Tue Jun 14 2005 - 07:18:20 CDT

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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