Re: "didn't find VdW parameter for atom type NH3" error

From: felmerino_at_uchile.cl
Date: Tue Jun 29 2010 - 21:20:47 CDT

I beg to disagree with peter, but it is a CG psf file. It uses the
residue based coarse grain. Yet, NH3 is the atom type in the N-term of
proteins and there is no reference to a NH3 atom in your psf. It seems
that you have somehow confused some CG with all atom structures.

PS:
If you are using the parameters set that cames with vmd remember that
this model was in principle parametrized in a way that it preserves
secondary structure elements (mostly helices) very, well but the same
is not necessarily true for terciary contacts. In our lab we have seen
that the dihedral basin for helices (look the parameters file) is
overestimated and you may need to create an ad hoc set of dihedral
parameters for your specific case.

best

Felipe

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