restrained MD

From: Vlad Cojocaru <>
Date: Wed 04 Dec 2002 19:18:54 +0100

Dear Amber users,
    I want to model an RNA stem-loop. The stem already exists in a
crystal structure. I want to run some simulating annealing using as
restraints the values of distances and angles from the crystal
structure. But the problem is that I only have a pdb file from the
crystal structure and programs like makeDIST_RST and makeANG_RST need
also other input apart from a pdb file. Does anyone have anysuggestions
how can I create the restraint files for sander input?
Thanks a lot for any advice,

Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1389 
home tel: ++49-551-9963204  
Received on Wed Dec 04 2002 - 10:18:54 PST
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