Dear all, I'd like to study intra-molecular hydrogen bonding. Which force field would you recommend?
I have been working on G43a1 and OPLS. OPLS seems quite good. It places all H-atoms. However, G43a1 only considers H-atoms on N-atoms, but not C-atoms. Even if I input a fully-added-H-atom PDB file to pdb2gmx: pdb2gmx -ff G43a1 -f 1eia_hadded.pdb -p 1eia.top -o 1eia.pdb -water spce 1eia.pdb still only constains H-atoms on N-atoms. I believe, by default, "-ignh" has value "no", which means if I don't put "-ignh", it should read in all the H-atoms in the input PDB file. Besides OPLS, is there any other good force field to study hydrogen bonding? Is there any way to make G43a1 to take all H-atoms into account? Thanks a lot! Peggy
_______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
