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

[MD]

Hi another quick question, what do you think could be the problem if the
modified amino acid is not connecting to the +1 amino acid? the [cmap ] in
merged.rtp already has the [ cmap ]    -C     N    CA     C    +N

Ming

On Mon, Jan 15, 2018 at 3:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

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