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

[MD]

whooops, never paid attention to the C N+, my bad, thank you Justin :)
Ming

On Mon, Jan 15, 2018 at 6:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/15/18 6:36 PM, MD wrote:
>
>> Sorry I didn't mean to connect it to the cmap. Yes it is a different
>> question. How do I define a bond to the +1 residue please? It is a side
>> chain modified amino acid (LYS) and the backbone is unchanged. What else
>> do
>> I need to take care to make sure the backbone still connects?
>>
>
> You need a bond between C and +N (see any other amino acid in the .rtp
> file to check your work).
>
> -Justin
>
>
> Thanks a bunch,
>>
>> Ming
>>
>> On Mon, Jan 15, 2018 at 6:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>> 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
>>>
>>> ==================================================
>>>
>>> --
>>> 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
>
> ==================================================
>
> --
> 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.
>