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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 10 2009 - 01:17:07 PDT
