[gmx-users] Adding residue to .rtp file

[Justin Lemkul]

On 10/4/18 2:11 PM, Raji wrote:
>> Okay. Then this custom residue(aminoacid+Alkyl chain) can be parameterized
>> with swissparam? and can be added as new residue in .rtp file?

Never used it, so I can't vouch for its accuracy. But stitching an alkyl 
group to an existing amino acid should be very straightforward without 
having to parametrize the entire molecule, which is what any server is 
going to try to do.

-Justin

>
> Thanks
> Raji
>
>
>
>
>>
>> ----------------------------------------------------------------------
>>
>> Date: Thu, 4 Oct 2018 11:36:22 -0400
>> From: Justin Lemkul <jalemkul at vt.edu>
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] Adding residue to .rtp file
>> Message-ID: <967a7926-899c-ba14-36ef-22830d364bad at vt.edu>
>> Content-Type: text/plain; charset=utf-8; format=flowed
>>
>>
>>
>> On 10/4/18 11:28 AM, Raji wrote:
>>> Thank you for your reply. I am trying to simulate this peptide in gromacs
>>> with CHARMM36 force field. Thatswhy i converted the parameters from
>> CGenFF
>>> to CHARMM format. So How to proceed further.  I assume i cant treat it
>> like
>>
>> The first step is to not use CGenFF to parametrize the custom residue.
>>
>>> as a protein ligand complex, because there is covalent bond between TYR
>> and
>> It's just a protein, there is no ligand.
>>
>>> alkyl chain? And What is core CHARMM atom types?
>> By "core CHARMM atom types," I mean those that are already part of the
>> C36 force field, not coming from CGenFF. If the second character of the
>> atom type is "G" then you are using a CGenFF type. Don't.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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.thelemkullab.com
>>
>>
>>

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

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.thelemkullab.com

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