You probably want to use the "Amber7 restart" format in VMD. That is the
format of output from leap and sander/pmemd. VMD will likewise generally
fail to read files of any other format. I also always give files the
extension ".rst7" or use "-rst7 xxfilenamexx" in order to get VMD to read
the coordinates properly.
Regards,
Brian
On Thu, Mar 7, 2013 at 2:13 PM, Shashidhar Rao <shashidharr.gmail.com>wrote:
> Earlier I attempted to send this message together with the mdcrd file, but
> was "bounced". Hence I am re-sending the message without the mdcrd file.
>
> thanks,
> Shashi Rao
>
> ---------- Forwarded message ----------
> From: Shashidhar Rao <shashidharr.gmail.com>
> Date: Thu, Mar 7, 2013 at 2:09 PM
> Subject: failed to run sander ....
> To: AMBER Mailing List <amber.ambermd.org>
>
>
> Dear Amber Gurus,
>
> I am attempting to run sander on a MD trajectory, but the job dies with an
> error about not finding the number of atoms or the time on the second line
> of the inpcrd file. The output file of the failed run (min.out) is
> attached.
>
> the command that was executed looks like this (input file min.in and a
> gzipped version of the input trajectory are also attached):
>
> sander -O -i min.in -p ../1BIL_complex_changed.prmtop -c
> TRJ1_snapshots.mdcrd -o min.out -r junk.crd -x TRJ1_snapshots_min.mdcrd
>
> Here is how I obtained the mdcrd file:
>
> 1. ran MD using DESMOND
> 2. input the DESMOND trajectory along with the reference molecule into VMD
> 3. saved the trajectory coordinates in the "crd" file format
>
> Am I mistaken in thinking that the crd file format is the AMBER md
> coordinate file format?
>
> Any suggestions would be most appreciated.
>
> thanks,
> Shashi
>
>
>
> --
> Shashidhar N. Rao
> 3 SERINA DRIVE
> PLAINSBORO
> NEW JERSEY 08536 USA
>
> shashidharr.gmail.com
>
>
>
> --
> Shashidhar N. Rao
> 3 SERINA DRIVE
> PLAINSBORO
> NEW JERSEY 08536 USA
>
> shashidharr.gmail.com
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Thu Mar 07 2013 - 12:30:03 PST
