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

[MD]

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?

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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