[gmx-users] Help parameterizing ddb to work with vsite -h option of pdb2gmx

[Ilya Chorny]

Hi All,
I am trying to get pdb2gmx -vsite h to work for a sugar attached to my
protein. I am using non standard atom names to differntiate from the OPLS
atom names.  I have gone through the manual a few times and I don't
understand the relationship between the files. The ffoplsaa.ddb has bonds
between heavy atoms and not hydrogens. Why?

Thanks,

Ilya


-- 
Ilya Chorny Ph.D.
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