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

Justin Lemkul jalemkul at vt.edu
Mon Jan 15 21:10:16 CET 2018

On 1/15/18 3:06 PM, MD wrote:
> I wonder if there is a way I can create my own cmap for those modified type
> names and incorporate the cmap to the cmap.itp?

That will end up being far more work than a proper parametrization of 
the side chain while leaving the backbone alone at standard atom types 
and charges.


> Thanks,
> Ming
> On Mon, Jan 15, 2018 at 2:56 PM, MD <refmac5 at gmail.com> 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?
>> 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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