VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jan 03 2007 - 20:09:29 CST

Dear Nitin,
I'm attaching a recently modified version of NAMDenergy that uses amber
files instead of charmm; please find it attached to that email; just
source it prior to opening the namdenergy plugin during your vmd
session. The presence of an amber-based topology is automatically
detected. Please let me know if you have any problems. This capability
will be included in the next release of vmd 1.8.6.

I will also note that just in general, you should upgrade to vmd 1.8.5
and namd2.6 to get the best results with this plugin.

Best,
Peter

Nitin Bhardwaj wrote:
> Dear VMD users,
> I am trying to execute namdenergy to calculate energy with a dcd
> file that was created with amber format input (parm 7) ".prmtop" and
> ".inpcrd" files. But I do not know how do I specify this while running
> namdenergy. I tried to look at the code but could not get much.
>
> I have VMD1.8.3 on windows platform.
>
> thanks a lot in advance,
> rgds,
> Nitin