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

MD refmac5 at gmail.com
Mon Jan 15 21:06:36 CET 2018

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?

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

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