Re: AMBER: Moil-view & Amber trajectory

From: Carlos Simmerling <>
Date: Fri, 17 Sep 2004 17:01:37 -0400

does moil-view work on the file before you run it through ptraj?

were you careful with the box dimensions in the traj file?
ptraj can control whether the box is included or not.
visually inspect your trajectory file and compare it to the format
for traj files given on the amber site.

if the traj file matches the prmtop, moil-view works.

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:
=================================================================== wrote:

>Dear Amber community,
>I ran a simulation with the following input in Amber7:
> imin=0, irest=1, ntx=5,
> iwrap=1,
> ntb=2, ntp=1, pres0=1.013, taup=2.0,
> ntf=1,
> igb=0,
> ntr=0, cut=12,
> ntt=1, tempi=300.0, temp0=300.0, tautp=1.0,
> nstlim=30000, dt=0.001, t=20,
> ntpr=100, ntwx=100, ntwr=1000
>When the run is done, I combine the trajectory of this and a run before
>and after it using ptraj. The run before this had the solute restrained
>as it is outlined in the amber tutorial online.
>When viewing the trajectory as it progresses through time in moil-view
>(version 10.1) the molecules are all over the place, in the sense that
>the bonds are way too long.
>In ptraj I tried to just combine the trajectories (with and without the
>fixed solute run). Then I tried the image function (although it shouldn't
>be necessary, with iwrap=1, right?), still the same result.
>Why does moil-view, when viewing the trajectory (while it is making the
>movie), show such long bonds, instead of the right bonds of individual
>solvent and solute molecules?
>Best Regards,
>The AMBER Mail Reflector
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Received on Fri Sep 17 2004 - 22:53:01 PDT
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