Dear all,<br><br>I'd like to study intra-molecular hydrogen bonding. Which force field would you recommend?<br><br>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:<br>
<br>pdb2gmx -ff G43a1 -f 1eia_hadded.pdb -p 1eia.top -o 1eia.pdb -water spce<br><br>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.<br>
<br>Besides OPLS, is there any other good force field to study hydrogen bonding?<br><br>Is there any way to make G43a1 to take all H-atoms into account?<br><br>Thanks a lot!<br><br>Peggy<br>