Brian is right here- the issue is that VMD's Amber "coordinates" refers to
the trajectory file. Use the Amber restart format for viewing
single-structure coordinate files.
On Wed, Mar 5, 2014 at 9:46 AM, Brian Radak <radak004.umn.edu> wrote:
> 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 - 07:00:05 PST
