[AMBER] Fwd: failed to run sander ....

From: Shashidhar Rao <shashidharr.gmail.com>
Date: Thu, 7 Mar 2013 14:13:58 -0500

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




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Received on Thu Mar 07 2013 - 11:30:04 PST
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