[gmx-users] GROMOS atp file

[faride badalkhani]

Dear all,

I am having a question about Hydrogens in GROMOS FF. There are two
Hysrogens in .atp file of GROMOS FF as follows:

   HC   1.00800 ;     hydrogen bound to carbon
      H   1.00800 ;     hydrogen not bound to carbon

and all the nonbonded parameters for H are considered zero, but what about
polar Hydrogens that are bounded to elements other than C (for example H in
amino or amid groups)? How should I treat with these polar hydrogens?

Kind Regards,
Farideh