[gmx-users] atom types consistency between atb and charmm

[MD]

Hi Justin,

Then what would be the solution if I need to add a modified amino acid in
merged.rtp and ffbonded.itp I wonder? My amino acid will have a fairly
large ligand covalently bonded with.

Ming

On Thu, Jan 4, 2018 at 8:43 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/4/18 8:41 AM, MD wrote:
>
>> Hi Gromacs folks,
>>
>> I was using atb to generate topology files for my ligands and modified
>> amino acid and needed to change the atom types from atb output to make
>> them
>> consistent with charmm, the force field I used, since I need to include a
>> modified amino acid.
>>
>> I wonder if there is a way to change all the atom types systematically and
>> automatically or it is the only way to change them manually?
>>
>
> You can't combine anything from ATB (which is for the united-atom GROMOS
> force field) with CHARMM. Mixing and matching force fields is fundamentally
> invalid because they all rely on different assumptions, functional forms,
> etc.
>
> -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
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>
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