AMBER Archive (2004)

Subject: Re: AMBER: PMEMD and nmropt=1

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Feb 05 2004 - 15:45:07 CST

Kristina -
If you can give me a test case on this, I'll look at it. I know that group
data sometimes would not parse correctly under Amber 6, depending on the
order that you put things in. I sort of fixed some of this, but I don't
know if what you are seeing is something that is Amber 6-standard, something
I broke trying to fix other mdin ordering problems in 6, or what. Anyway,
given concrete input, I'll take a look.
Regards - Bob
----- Original Message -----
From: "Kristina Furse" <kristina.e.furse_at_vanderbilt.edu>
To: "Robert Duke" <rduke_at_email.unc.edu>; <amber_at_scripps.edu>
Sent: Thursday, February 05, 2004 4:19 PM
Subject: RE: AMBER: PMEMD and nmropt=1

> Just a note since I saw my name... I've been able to successfully use
nmropt=1
> with pmemd for the case where the nmr-style restraints are in a separate
file
> called with DISANG=restraintFile in the mdin. I have, however run into
> problems when I tried to use nmropt=1 and ntr=1 at the same time with
pmemd.
> It seems there is a problem parsing the mdin file when both types of
restraint
> methods are used simultaneously (the DISANG line is read as a title, or
> something like that). I didn't pursue it any farther than that (still
don't
> know if it was some error of mine, or program related, but the same file
does
> work with sander in amber7), but if it would help anyone, I could track
that
> problem more carefully.
>
> Kristina
>
> >===== Original Message From "Robert Duke" <rduke_at_email.unc.edu> =====
> >Aldo -
> >I am pretty much the "pmemd guy". If you are having a problem with
pmemd,
> >and the same input runs okay in sander 7, please send all input and
output
> >to me and I will debug the problem (also let me know what platform and
what
> >MACHINE file you used). With pmemd, nmropt=2 is not supported, but all
the
> >nmropt=1 options are supposed to work. However, getting test coverage of
> >everything done under nmropt=1 is a bear so there is the possibility of a
> >problem (I did not do much at all to change the nmr code, though). Also
let
> >me know your pmemd version.
> >Regards - Bob Duke
> >----- Original Message -----
> >From: "aldo jongejan" <jongejan_at_few.vu.nl>
> >To: <amber_at_scripps.edu>
> >Sent: Thursday, February 05, 2004 6:52 AM
> >Subject: AMBER: PMEMD and nmropt=1
> >
> >
> >> Dear all,
> >>
> >> I am trying to run similar jobs as I have ran with AMBER 7 in PMEMD,
> >> but am not able to get the jobs running. It seems that the nmropt=1
> >> option is causing the trouble, as jobs without these restraints ran
> >> smoothly.
> >> I have read the mails of Kristina Furst and Robert Duke, but my runs
> >> don't even get that far...they stop producing output after echoing the
> >> input-deck and the title of the run. The job hangs after this..
> >>
> >> Maybe something goes wrong in the calls to MPI, but I wondered
> >> if somebody could help me, before diving into the source code :-)
> >>
> >> greetings,
> >>
> >> aldo
> >>
> >> --
> >> ###########################################
> >>
> >> Aldo Jongejan
> >> Molecular Modeling Group
> >> Dept. of Pharmacochemistry
> >> Free University of Amsterdam
> >> De Boelelaan 1083
> >> 1081 HV Amsterdam
> >> The Netherlands
> >>
> >> e-mail: jongejan_at_chem.vu.nl
> >> tlf: +31 (0)20 4447612
> >> fax: +31 (0)20 4447610
> >>
> >> ###########################################
> >>
> >>
> >>
> >>
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> >>
> >>
> >
> >
> >
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> ****************************************************
> Kristina E. Furse
> Department of Chemistry
> Center for Structural Biology
> Vanderbilt University
> email: kfurse_at_structbio.vanderbilt.edu
>
>
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>

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