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

[Justin Lemkul]

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
>>>>>
>>>>> ==================================================
>>>>>
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>> --
>> ==================================================
>>
>> 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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>> Gromacs Users mailing list
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-- 
==================================================

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

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