[gmx-users] Question

Davoud Zare davoud1983 at yahoo.com
Tue Oct 23 08:18:00 CEST 2012

Dear Sir
I am a newbie on Gromacs. I am trying to solvate my protein (1CJ5.pdb) with water. I am following the tutorial by Justin Lemkul but when I execute the following command
pdb2gmx -f 1CJ5.pdb -o 1CJ5_processed.gro -water spce

and choose OPLS-AA/L all-atom force field 
I am getting an fatal error 
Fatal error:
Atom HB3 in residue TYR 2 was not found in rtp entry TYR with 21 atomswhile sorting atoms.
any comments on that?
I would like to know about the protein adsorption energy and conformational changes at water-hexane interface, would appreciate if any one could possibly take the time and let me know what should I do to do this in Gromacs
Thank you


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