AMBER: Nmode with residues excluded

From: Martin Sippel <>
Date: Fri, 3 Jun 2005 18:56:42 +0200 (MEST)

Hi Amber community,

I want to do some nmode calculations on my protein-ligand-complex. For this purpose I only choose residues which are
within a 10A radius of the mass center of the ligand. How can I create an adequate prmtop-file? The mm_pbsa script in
Amber8 gave an error message when I used the prmtop-file for the whole complex.

Thanks for any comments!



Martin Sippel
Max-Planck-Institute for Biophysical Chemistry
NMR-based Structure Biology, Office 5
Am Fassberg 11
37077 Göttingen

Tel.: +49 551 201 2215

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Jun 03 2005 - 18:53:00 PDT
Custom Search