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

[MD]

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
>