[gmx-users] gromacs.org_gmx-users Digest, Vol 174, Issue 10

[Raji]

> Okay. Then this custom residue(aminoacid+Alkyl chain) can be parameterized
> with swissparam? and can be added as new residue in .rtp file?


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
>
>
>