VMD-L Mailing List

From: Per Jr. Greisen (pgreisen_at_gmail.com)
Date: Sun Oct 28 2007 - 04:56:03 CDT

Hi,

You can download them here:

http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm

On 10/28/07, Per Jr. Greisen <pgreisen_at_gmail.com> wrote:
>
> Hi,
>
> You can download them here:
>
> http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm
>
> On 10/28/07, Samuel Flores <samuel.flores_at_yale.edu> wrote:
> >
> > Hi Guys,
> >
> > Thanks again for the last answer.. haven't touched NAMD in the
> > longest time. I have an additional question..
> >
> > I am trying to model RNA. I see in the archives that I need
> > par_all22_prot_na.inp and top_all22_prot_na.inp . However I can't
> > find these anywhere! Can you tell me where I can get them?
> >
> > Sam
> >
> >
> > On Oct 26, 2007, at 10:22 AM, Axel Kohlmeyer wrote:
> >
> > >
> > > On Fri, 26 Oct 2007, Samuel Flores wrote:
> > >
> > > SF> Hi Guys,
> > >
> > > hi sam,
> > >
> > >
> > > SF> I wonder if someone could remind me how to play back NAMD
> > > trajectories in
> > >
> > > why don't you remind yourself by looking at the stuff at:
> > > http://www.ks.uiuc.edu/Research/vmd/current/docs.html#tutorials
> > > ?
> > >
> > > SF> VMD. I thought I would just load the .pdb, .psf, and .dcd
> > > files and hit
> > > SF> "play." The protein looks fine but when I load the .dcd file
> > > and hit play i
> > > SF> see a bunch of white dots dancing around a static pdb
> > > structure. Can anyone
> > > SF> tells me what I'm doing wrong?
> > >
> > > you load the .psf file first and then the .dcd file "into"
> > > this molecule. the .psf file contains the topology information
> > > and atom names etc., the .dcd only the coordinates. you need
> > > both for a proper display.
> > >
> > > cheers,
> > > axel.
> > >
> > > SF>
> > > SF> Sam
> > > SF>
> > >
> > > --
> > > ======================================================================
> >
> > > =
> > > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://
> > > www.cmm.upenn.edu
> > > Center for Molecular Modeling -- University of Pennsylvania
> > > Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> > > 19104-6323
> > > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> > > ======================================================================
> >
> > > =
> > > If you make something idiot-proof, the universe creates a better
> > > idiot.
> >
> >
>
>
> --
> Best regards
> Per Jr. Greisen
>
> "If you make something idiot-proof, the universe creates a better idiot."
> 

-- 
Best regards
Per Jr. Greisen
"If you make something idiot-proof, the universe creates a better idiot."