[gmx-users] Which force field to use to study intra-molecular hydrogen bonding?

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 18 00:43:22 CET 2009

Peggy Yao wrote:
> 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:

Right, because the Gromos force fields are united-atom.

> 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.

It should also contain H atoms on other polar groups (-OH, etc), as well as 
aromatic rings.

> Besides OPLS, is there any other good force field to study hydrogen bonding?

Hydrogen bonds are calculated by geometry.  Do a few tests to see which force 
field you believe.

> Is there any way to make G43a1 to take all H-atoms into account?

No, it is a united-atom force field.


> Thanks a lot!
> Peggy
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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