VMD-L Mailing List

From: Samuel Flores (samuel.flores_at_yale.edu)
Date: Sun Oct 28 2007 - 03:23:39 CDT

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.