AMBER Archive (2009)

Subject: [AMBER] Sander and multiple residues

From: Dan Kaps (dan.kaps_at_yahoo.com)
Date: Thu Apr 09 2009 - 13:48:55 CDT

Hello All,
I am attempting to run a molecular dynamics simulation in Sander. I have a chain of three benzene rings with a water molecule above the center benzene ring (residues UNK and AGT). I used leap to get .prmtop and .inpcrd files for both residues. Although I'm not sure if this is valid, I combined the separate .prmtop and .inpcrd into one .prmtop and one .inpcrd file. When I ran sander, it completely ignored the presence of AGT. Does anyone have any suggestions?
Thanks,
Dan Kaps

      
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