[gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer

[Justin Lemkul]

On 11/20/19 8:51 PM, Mijiddorj B wrote:
> Dear Prof. Justin,
>
> Thank you very much for your reply. I would like to use charmm27 because my
> system contains a surface model, which were parametrized by INTERFACE Force
> Field and compatible with charmm27. The polymer parameters of charmm27 were

AFAIK there's no reason to believe you have to use CHARMM27; INTERFACE 
is generally compatible with CHARMM, which has a linear development 
history so you should be able to combine it with any CHARMM potential.

> generated by swissparam, and the server renamed the atomtypes. I would like
> to assign those parameters with original charmm27. If possible, I would
> like to use original charmm27 parameters instead of the values of
> swissparam. I used charmm36 atomtypes for clarification.
> I do not know the atom type of the nitrogen which connected with three
> carbons.

NG301. I still think it's best if you simply parametrize your monomer 
units with CGenFF and use its parameters unless there are major penalties.

-Justin

>
> Best regards,
>
> Mijiddorj
>
> ------------------------------
>> Message: 5
>> Date: Wed, 20 Nov 2019 20:19:16 -0500
>> From: Justin Lemkul <jalemkul at vt.edu>
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] Charmm27 and Charmm36 atomtypes assignments
>>          for polymer
>> Message-ID: <7db2548d-f487-a34b-f27f-0f876aa202ca at vt.edu>
>> Content-Type: text/plain; charset=utf-8; format=flowed
>>
>>
>>
>> On 11/19/19 9:54 PM, Mijiddorj B wrote:
>>> Dear Gmx users,
>>>
>>> Currently, I am trying to assign the atomtypes in charmm27 for the
>>> polyethyleneimine polymer. It includes several different groups of
>> atoms. I
>>> included following illustration and asignment:
>>> ##############################################
>>>                            H                     CH2
>>>                            |                     /
>>> NH2--CH2--CH2--N--CH2--CH2--N--CH2 ...
>>>
>>> ##############################################
>>> I assigned and the charmm27 atomtypes as following and compared charmm36
>>> atomtypes generated by CgenFF.
>>> Atom       Charmm27     Charmm36
>>> N (NH2) ---> NH2       |    NG321
>>> N (NH1) ---> NH1       |    NG311
>>> C (CH2) ---> CT2       |    CG321
>>> H (HC2) ---> HA         |    HGA2
>>> N                 ?           |    NG301
>>>
>>> If you have any experience, please check my assignments the charmm27 atom
>>> types and advice me the atomtype of the last Nitrogen, which were
>> assigned
>>> as NG301 with CgenFF.
>> Why are you replacing the CGenFF atom types? The replacements you are
>> making completely change the LJ terms and therefore render the dihedral
>> parameters invalid. There is no need to make these changes, just use the
>> CGenFF atom types in your simulation (all of which is contained in the
>> CHARMM36 port, which you should use rather than the outdated CHARMM27
>> force field files).
>>
>> -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 49
>> ******************************************************
>>

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

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

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