AMBER Archive (2004)

Subject: Re: AMBER: Moil-view & Amber trajectory

Date: Mon Sep 20 2004 - 16:59:39 CDT

('binary' encoding is not supported, stored as-is) The same problem occurs when using the trajectory with and without
running it through ptraj.

I did not do anything about the box dimensions in ptraj.
Is there something I have to do to the coordinates? I start the system
with solute and let it equilibrate to pressure. Obviously that changes
the dimensions of the box. Would the treatment with ptraj have to involve
a step that accounts for this?
Please advise.

Best Regards,


==============Original message text===============
On Fri, 17 Sep 2004 17:01:37 EDT Carlos Simmerling wrote:

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: 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?

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