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

[Justin Lemkul]

On 1/15/18 6:25 PM, MD wrote:
> 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.

That has nothing to do with CMAP, that means you didn't properly define 
a bond to the +1 residue.

-Justin

> 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
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>

-- 
==================================================

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

==================================================