AMBER Archive (2004)

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

From: Carlos Simmerling (
Date: Tue Sep 21 2004 - 11:17:59 CDT

Did you carefully check the format of your file compared to the
format listed on the amber web page? I asked this before but you didn't
reply. Also, if it is a periodic simulation, make sure to choose "AMBER PBC"
as the trajectory file format (it should describe this in more detail in
the moil-view

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:

>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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