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

[Justin Lemkul]

On 5/25/17 3:12 PM, Gilberto Valdes wrote:

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.


Use our CHARMM36 port:

http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

It has ATP, from which you can easily make an AMP unit linked to lysine.  You'll 
likely have to parametrize the linkage.  This will involve a geometry 
optimization, charge assignment (most can be taken by analogy, just a few atoms 
around the linkage should change), water interactions, a bonded refinement 
including potential energy scans for dihedrals.  You can probably use CGenFF as 
a starting point but you should ultimately not mix general atom types with 
protein and nucleic acid types.


-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [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 :

>
>
> 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
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] simulating AMP covalently linked to a protein

[Justin Lemkul]

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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