AMBER Archive (2002)

Subject: Re: Visualizing AMBER coordinates trajectory in VMD

From: Tom Bishop (bishop_at_tulane.edu)
Date: Tue Nov 05 2002 - 05:36:41 CST

Dear VMD-amber users,

You should also be aware of the following "sync" issue when reading crds
into vmd

If I generate an old style crd using leap it has the following header
information
cholestane 77% head -2 sys.crd

 4016

while vmd prefers to read the following
cholestane 78% head -2 vmd.crd
 4016
   0.3470000 -0.2170000 -5.8050000 0.6483152 0.7044259 -6.0503232

Notice the blank or title line in the leap generated crd.
However if I use a crd formatted trajectory generated from sander there
is only one blank line
and vmd can reads this as a trajectory.
cholestane 104% head -2 eq.2.crd
                                                                                
  29.403 24.430 32.985 29.697 25.084 32.348 29.440 25.056
34.192 28.270

Solution.
When I make a parmtop with leap I make sure to save a copy in the old
style format and
and I make a copy of the initial crd w/out the first line by running the
following command after
all of my tleap scripts.
awk '{ if (NR != 1 ) print $0 } ' sys.crd > vmd.crd

Cheers,
TOm

"David A. Case" wrote:
>
> On Mon, Nov 04, 2002, Pratul Agarwal wrote:
> >
> > Is it possible to use VMD to visualize an AMBER trajectory (generated by
> > sander), which has only solute coordinates saved? My system has explicit
> > solvent but to save disk space I only saved the solute coordinates. When
> > I load the parm and crd file in VMD, the display looks strange, my guess is
> > that this is because of missing solvent coordinates. Is there any way to fix
> > this?
>
> You should be able to construct a modified prmtop file in one of two ways:
>
> (a) go back to your LEaP script, and re-run, omitting any "solvate" and
> "addIons" commands.
>
> (b) use rdparm, with the commands "stripwater" and "writeparm".
>
> Then you should have a prmtop file that has not waters, and hence is "in sync"
> with the trajectory file.
>
> ..good luck...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ================================================================== 

-- 
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Thomas C. Bishop, Ph.D.
Joint Faculty Appointments Program Professor
Center for Bioenvironmental Research
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