[AMBER] Amber and gaff atom types

From: Aditya G Rao <aditya.grao.mail.huji.ac.il>
Date: Fri, 14 Oct 2016 00:12:18 +0300

Dear all,

I'm facing a similar problem as Miha's at the moment. The protein I want to
study has a large chromophore covalenty bound to a cysteine residue. So I
want to create a new modified residue to run the simulations. For this
purpose I followed the Amber Tutorial B5 (GFP) until the parmchk2 call in
the middle of Section 3. Then I faced the same problem as Miha, because
some of the atom types are already available in protein ffs (ff14SB) but
others are not. (Atom types CX, 2C, 3C and CO were not present
in Parmchk.dat)

Is it problematic to mix atom types from gaff with the classical protein
ff? If I understood Miha correctly, he is also working with a protein.

.David: what do you mean by "in most cases, it will be better to do this
job by hand"? Miha wrote in his email that he changed the atom type by hand.

Thanks for your help,

Aditya G. Rao
PhD Student
Fritz Haber Research Center for Molecular Dynamics
Institute of Chemistry, HUJI
Givat Ram, Jerusalem, Israel
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Received on Thu Oct 13 2016 - 14:30:03 PDT
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