AMBER Archive (2005)

Subject: AMBER: Nmode with residues excluded

From: Martin Sippel (masi_at_nmr.mpibpc.mpg.de)
Date: Fri Jun 03 2005 - 11:56:42 CDT

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!

Regards,

Martin

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

Tel.: +49 551 201 2215

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