[gmx-users] simulating AMP covalently linked to a protein

[Gilberto Valdes]

Thanks for your answer,
I would like to use charmm27 force field, it covers the hole AMP molecule
if I use the ADE residue with the 5PHO and 3TER patches implemented in
charmm software.
The problem is how to patch the ADE equivalent residue (named RA) in
gromacs, and then how to linked to the epsilon N group of the Lys.
greets Gilberto

2017-05-25 13:55 GMT-05:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 5/24/17 7:08 PM, Gilberto Valdes wrote:
>
>> Hi,
>>
>> I'm interested in simulating a DNA ligase with an AMP bound covalently via
>> its P atom to the side chain of a Lysine residue. I can not find any
>> parameters for that. I really appreciate any help in how to achieve this.
>>
>>
> http://www.gromacs.org/Documentation/How-tos/Parameterization
>
> The details depend on which force field you've chosen to use, and that
> choice actually depends on other factors - how much chemical space that
> force field covers (e.g. how easy is it going to be to even start this
> venture) and how easy to follow are the published methods for that force
> field.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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