AMBER Archive (2004)

Subject: RE: AMBER: PMEMD and nmropt=1

From: Kristina Furse (kristina.e.furse_at_vanderbilt.edu)
Date: Thu Feb 05 2004 - 15:19:52 CST

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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