[gmx-users] atom types consistency between atb and charmm
refmac5 at gmail.com
Thu Jan 4 18:20:03 CET 2018
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.
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
>> 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,
> 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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