VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Tue Oct 30 2007 - 13:30:26 CDT

Thanks a lot! It works just fine!
 
Irene
> Date: Fri, 26 Oct 2007 15:50:55 -0500> From: johns_at_ks.uiuc.edu> To: einew_at_hotmail.com> CC: vmd-l_at_ks.uiuc.edu> Subject: Re: vmd-l: how to display dcd file written with catdcd using an index file> > > Hi,> You'll need to perform the same slicing and dicing on the main> structure file as you've done on the DCD, so that you can load the> DCD with the new structure to view the simulation. Since you're working> with AMBER inputs, you may find it easiest to do this by using> atom selections to chop the same portions of the structure you chopped> using catdcd, and writing it out to a new PDB/PSF pair. Once you've> got those, then you can load the PDB, PSF, and DCD into VMD and everything> should work fine. The PSF generated by this operation won't be useful> for simulation since it will have lost the angles/dihedrals/impropers etc,> but it will preserve the same bonding information that was in your original> AMBER data, but for the selected subset of atoms.> > Cheers,> John Stone> vmd_at_ks.uiuc.edu> > On Fri, Oct 26, 2007 at 09:08:44AM -1000, Irene Newhouse wrote:> > > > I've simulated a fairly large system & would like to look at only a particular region, so I did a web search & was able to find out how to write an index file to use in catdcd, to select only the portion of interest. Now I'm stuck a simpler problem - what files do I load into VMD to let me animate the resultant file? I had a web page at one point which might have helped, but I lost the URL & try as I might, can't recover it.> > > > Incidentally: I'm using AMBER inputs, as the ligand to my protein is a saccharide for which there aren't good CHARMM parameters, while there's GLYCAM for AMBER, which has a literature base behind it.> > > > Thanks!> > Irene Newhouse > > _________________________________________________________________> > Windows Live Hotmail and Microsoft Office Outlook – together at last. Get it now.> > http://office.microsoft.com/en-us/outlook/HA102225181033.aspx?pid=CL100626971033> -- > NIH Resource for Macromolecular Modeling and Bioinformatics> Beckman Institute for Advanced Science and Technology> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
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