VMD-L Mailing List

From: Philip Fowler (p.w.fowler_at_qmul.ac.uk)
Date: Tue Feb 22 2005 - 10:06:55 CST

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