[gmx-users] polymer charmm27 parameter

[Justin Lemkul]

On 11/18/19 12:12 AM, Mijiddorj B wrote:
> 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?

No. Use self-consistent topologies. Charge assignment affects dihedrals, 
so if you have different charges from each server, your dihedrals are no 
longer consistent.

-Justin

> 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
>>>
>>> ==================================================
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> --
>>> 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.
>>>
>>> End of gromacs.org_gmx-users Digest, Vol 187, Issue 28
>>> ******************************************************
>>>

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

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

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