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

[MD]

I mean it is disconnected after energy minimization, i found out the CO is
not connecting with the NH from the +1 amino acid. The structure was intact
before the simulation.

Ming

On Mon, Jan 15, 2018 at 6:23 PM, MD <refmac5 at gmail.com> wrote:

> 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
>>>>
>>>>
>> --
>> ==================================================
>>
>> 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
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
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>
>