[gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

Justin Lemkul jalemkul at vt.edu
Mon Jan 15 21:09:47 CET 2018

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.


> Thanks,
> Ming
> On Mon, Jan 15, 2018 at 1:34 PM, MD <refmac5 at 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


Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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