VMD-L Mailing List

From: Justin Gullingsrud (justinrocks_at_gmail.com)
Date: Tue Feb 22 2005 - 13:22:26 CST

Hi,

I've used the Gromacs programs g_covar and g_anaeig to perform
analysis of NAMD-generated trajectory files by first converting the
trajectory to sequential pdb format. You can do this in VMD by simply
loading the dcd file and saving it as a pdb, but there is one caveat:
you must change all the "END" lines to "ENDMDL", or g_covar will
crash.

Hope this helps,
Justin

On Tue, 22 Feb 2005 16:06:55 +0000, Philip Fowler <p.w.fowler_at_qmul.ac.uk> wrote:
> Hi everyone,
>
> I really, really want to use the IED plugin for VMD
>
> http://mccammon.ucsd.edu/ied/
>
> to analyse the principal components of my molecular dynamics simulations. But
> I use NAMD (naturally) and I am having difficulty pre-processing the
> trajectories using PTRAJ as recommended by the developers of IED. I have
> tried both the freely available PTRAJ and the one that is part of the
> AMBER8.0 package and each time it does not like reading my NAMD CHARMM .psf
> topology file. (Error: "WARNING in scanDouble: ...scanning LES, lesfac")
>
> Has anyone successfully managed to use IED to analyse NAMD trajectories (with
> the CHARMM forcefield)?
>
> Are VMD psfgen produced CHARMM .psf topology files incompatible with PTRAJ? I
> haven't even been able to try out a NAMD .dcd file yet.
>
> Any help would be greatly appreciated,
>
> Thanks,
>
> --Phil
>
> --
> Philip Fowler,
> PhD Student
> Centre for Computational Science,
> UCL Chemistry
> 

-- 
The spirit of Plato dies hard.  We have been unable to escape the
philosophical tradition that what we can see and measure in the world
is merely the superficial and imperfect representation of an
underlying reality.
                -- S.J. Gould, "The Mismeasure of Man"