This might actually be a question for the VMD guys, but I'll add my 2 cents.
First of all, in general AMBER rst7 files do not necessarily contain
velocity information (see the AMBER formats page).
In my experience the VMD plugins for the inpcrd format are a bit shaky
(although I think this is really a matter of incorrect expectation). They
sometimes read the number of atoms as the x coordinate of the first atom,
which is why you'll see one atom way outside the box with a long bond. I
don't know if this is because the format was changed at some point or
what.
In any event, you can almost always open inpcrd files as the rst7 format.
You can force VMD to do that by just naming all of your files with the rst7
extension, or use the -rst7 flag on the command line. You can of course
select AMBER restart 7 from the GUI too, but I rarely use the GUI for
loading lots of files.
Regards,
Brian
On Wed, Apr 18, 2012 at 3:21 PM, Aron Broom <broomsday.gmail.com> wrote:
> First, open your inpcrd file and go to the bottom and see if you actually
> have a line describing the periodic conditions (lengths and angles). If
> so, it's probably the way you opened it, an inpcrd file is not an AMBER
> restart file, the restart file contains velocity information also. You
> should open it as AMBER periodic coordinates, or something of the sort.
> All those options should be right next to each other in VMD, so it's
> surprising that you would have chosen the restart.
>
> Also, I think you want to open the prmtop first, and then load the inpcrd
> into that.
>
> ~Aron
>
> On Wed, Apr 18, 2012 at 3:16 PM, Albert <mailmd2011.gmail.com> wrote:
>
> > Dear:
> > I've built an md system with tleap by following command:
> >
> > tleap -s -f leaprc.ff99SBildn
> > source leaprc.gaff
> > loadamberparams ligand_AC.frcmod
> > loadoff ligand_AC.lib
> > mol = loadpdb complex.pdb
> > solvatebox mol TIP3PBOX 11.0
> > charge mol
> > addions mol Na+ 42
> > addions mol Cl- 30
> > charge mol
> > set default FlexibleWater on
> > saveamberparm mol bm.prmtop bm.inpcrd
> >
> > After than I open the solvated system in VMD:
> >
> > new molecule --> bm.inpcrd (amber 7 restart)
> > load --> bm.prmtop (amber7 parm)
> >
> > everything seems to be ok in VMD molecule viewer window. However, when I
> > try to open the periodic cell, nothing happen.... what I found is: all
> > Self, +x +y, +z are in the same position which responsible for that I
> > see "no periodic" cell because they overlap with each other......
> >
> > I also try to type
> >
> > pbc box
> >
> > in VMD terminal, and it said:
> >
> > -error Suspicious pbc side length (a=0.000000 b=0.000000 c=0.000000).
> > Have you forgotten to set the pbc parameters?
> >
> > Does anybody have any idea what happen?
> >
> > thank you very much
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
> _______________________________________________
> 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 Apr 18 2012 - 13:00:04 PDT
