On 1/15/18 2:56 PM, MD wrote:
updated, I figured it is because my N and CA have different type names than
charmm, which is weird cause I used CHARMM GUI to get the itp files for the
modified amino acid. Would it be an easy fix if I manually change those two
atom names or I should go a different route for the cmap problem?
CHARMM-GUI can only parametrize a species via the interface to CGenFF.
This is not appropriate for integral residues in a polypeptide chain.
The backbone of each amino acid is the same; yours has different atom
types (presumably from CGenFF) that are not the same as the normal
types. This makes the application of CMAP parameters impossible.
You should separately parametrize your side chain using CHARMM atom
types; the initial charges provided by CGenFF can be used as a first
guess but should be subject to refinement as needed. A proper
parametrization protocol will involve vibrational analysis, dipole
moment analysis, water interactions, and conformational energy scans. It
is laborious but if you want a custom residue to be consistent with the
highly optimized protein force field, you have to do the work.
-Justin
Thanks,
Ming
On Mon, Jan 15, 2018 at 1:34 PM, MD <refm...@gmail.com> wrote:
Hi Gromacs folks,
I have a modified amino acid which has all the parameters set. However,
the last error is the "cmap torsion between atoms xxxxxxx" and it would't
go away. Basically the cmap contains atoms of C-N-CA-C-N from three
residues, where the CA is my newly modified residue. THe only thing I could
think of is the newly modified residue was not recognized by gromacs, but I
have checked the residue.dat, the log from pdb2gmx and it looks like this
residue was not considered "alien". Got stuck here any help will be
appreciated!
Best,
Ming
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