The VMD formats for AMBER coordinates are quite old (I would hazard to call
them legacy formats). The problem is that the number of atoms gets read in
as the x coordinate of the first atom or something like that.
You want to use the "AMBER7 Restart" option for all coordinate files
generated by leap, sander, or pmemd. I would strongly recommend naming all
inpcrd (-c) and restrt (-r) files with the ".rst7" extension. Alternatively
you can load them on the VMD command line as "-rst7 *filename*".
Regards,
Brian
P.S. In the past I've made a little bit of noise on the VMD listserv about
this, but the bottom line is that there is no bug in the VMD code. The
default is just not necessarily what one would expect now that AMBER users
have developed the bad habit of naming one file format with several
different extensions. The new NetCDF restart format doesn't help this
situation much either (and is not supported by VMD at present).
On Wed, Mar 5, 2014 at 8:48 AM, DEBOSTUTI GHOSHDASTIDAR <
debostutighosh.gmail.com> wrote:
> Dear Prof Case and Jason
>
> Thanks for the prompt reply
>
> I am using VMD for visualizing.
>
> 1) I start VMD
> 2) New Molecule -> ADNA.top (leap generated) (format:Amber7parm)
> 3) Load data into molecule -> ADNA.crd (leap generated) (format: Amber
> coordinates with periodic box)
>
> And the entire structure appears distorted. Sorry for the confusion. The
> structure is distorted at this stage itself. I have attached a snapshot. I
> did not use solvateBox. I packed water with packmol and used the set
> command for dimensions.
>
> As suggested by Jason, I checked the restraint energy in the 1st step of
> minimization, it is 70.73kcal/mol (the rk2 value I gave was 100.0, I know
> its kind of high but I was just changing the force constant to see if
> things improve before I figured out the starting structure itself was
> distorted). There are no overlaps either as checked with the mentioned
> command.
>
> Thanks
>
>
>
> On Wed, Mar 5, 2014 at 6:47 PM, David A Case <case.biomaps.rutgers.edu
> >wrote:
>
> > On Wed, Mar 05, 2014, DEBOSTUTI GHOSHDASTIDAR wrote:
> > >
> > > I went a step back and visualized the leap
> > > generated pdb and it was a perfect A-DNA. However, when I loaded the
> leap
> > > generated crd file on the leap generated topology file, the structure
> > > looked severely distorted.
> >
> > This should not happen. The coordinates leap puts into the pdb file
> > should be the same as those it puts into the crd file. (If you are using
> > solvateBox, add "set default nocenter on" at the top of your leap.in
> > file.)
> >
> > It sounds like the problem is at the LEaP step: if you start with a
> > severely
> > distorted structure, you are indeed likely to have problems. You need to
> > try
> > to figure out what is going wrong at this early step.
> >
> > > I guess the A-DNA structure was disturbed during minimization.
> >
> > This is confusing: above you said you were seeing distortions with the
> > "leap generated crd file on the leap generated topology file". If so,
> bad
> > things must have happened before any minimzation.
> >
> > >
> > > For re-confirming, I visulalized the leap generated crd and topology
> > files
> > > given in the Amber tutorials Section B1 (Simulation of DNA) and even
> that
> > > structure was distorted. Where am I going wrong?
> >
> > What visualization program are you using? Exactly what commands are you
> > executing? The problem may be in how you are using the visualization
> > program,
> > but we can't help there, since we don't even know which program you are
> > using.
> >
> > ...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Debostuti
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Wed Mar 05 2014 - 07:00:04 PST
