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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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