[gmx-users] polymer charmm27 parameter

[Mijiddorj B]

Dear Justin,

Thank you very much for your reply.
I prepared 3 residues including a middle and two end units for charmm27. I
also used the swissparam for their atom type and the partial charges. Now,
Gmx pdb2gmx is working fine with the residues. Is it right?
However, grompp needs to set the bonds, angles, dihedrals, and improper
parameters of those atomtypes in charmm27 force field. Swissparam named the
atomtypes completely different from charmm27 force field. And I would like
to ask a question.
Can I use the parameter values generated by CgenFF with charmm22 force
field instead the values of swissparam?
Thank you again.

Best regards,

Mijiddorj


------------------------------
>>
>> Message: 5
>> Date: Mon, 11 Nov 2019 20:16:27 -0500
>> From: Justin Lemkul <jalemkul at vt.edu>
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] polymer charmm27 parameter
>> Message-ID: <76526271-8832-1f53-877a-6fceb6206044 at vt.edu>
>> Content-Type: text/plain; charset=utf-8; format=flowed
>>
>>
>>
>> On 11/11/19 10:05 AM, Mijiddorj B wrote:
>> > Dear Prof. Justin,
>> >
>> > Thank you very much for your reply. My target polymer is the branched
>> > polyethyleneimine. I copied a figure. I am sorry for furthermore
>> asking. If
>> > I understand correctly, the model compound consists of the last two
>> heavy
>> > atoms and first two heavy atoms along with the corresponding protons.
>> Is it
>> > right?
>>
>> Whatever model compounds you use have to encompass all relevant internal
>> degrees of freedom (bonds, angles, dihedrals).
>>
>> > Do I need to make a model N and C terminal atoms?
>>
>> You need termini, but N- and C-termini are protein-specific concepts, so
>> no, not exactly. See e.g.
>>
>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html
>>
>> -Justin
>>
>> > Thank you for your time.
>> >
>> > [image: image.png]
>> >
>> > Best regards,
>> >
>> > Mijiddorj
>> >
>> >> ----------------------------------------------------------------------
>> >>
>> >> Message: 1
>> >> Date: Sun, 10 Nov 2019 09:20:52 -0500
>> >> From: Justin Lemkul <jalemkul at vt.edu>
>> >> To: gmx-users at gromacs.org
>> >> Subject: Re: [gmx-users] polymer charmm27 parameter
>> >> Message-ID: <4ed3e913-bf3d-f79d-e997-fc03d451edcd at vt.edu>
>> >> Content-Type: text/plain; charset=utf-8; format=flowed
>> >>
>> >>
>> >>
>> >> On 11/10/19 8:52 AM, Mijiddorj B wrote:
>> >>> Dear GMX users,
>> >>>
>> >>> I would like to simulate a long polymer, which consists of the number
>> of
>> >>> units (monomers). I generated the charmm27 parameter for the single
>> unit
>> >>> using swissparam server.
>> >>> However, I need to prepare the parameter for the long polymer chain.
>> >>> If you have any experience, please advise me to build the topology of
>> the
>> >>> long polymer using the parameter of the single unit. Thanks for any
>> >>> guidance.
>> >> You need a model compound that captures all relevant degrees of
>> freedom,
>> >> including bonds, angles, and dihedrals between monomer units. You then
>> >> need to parametrize those interactions so the properties of your chain
>> >> are correct.
>> >>
>> >> -Justin
>> >>
>> >>
>> >
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>>
>>
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>>
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>> End of gromacs.org_gmx-users Digest, Vol 187, Issue 28
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>