[gmx-users] Umbrella sampling of phosphate ion binding

[bharat gupta]

Actually, I am planning to use AMBER forcefield for both phosphotyrosine and
for the system too. The parameters are reliable as they have been published
(http://www.springerlink.com/content/u527364w03568353/fulltext.pdf) . But I
want to know how to add them to the force field. I have checked the
following link :-
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field,
but I want  to do it in a rather shorter way. Like what has been done in the
protein ligand tutorial. But will that be ok to do. As in my case also I too
have a docked complex .

On Wed, Jun 8, 2011 at 10:26 PM, Dallas Warren <Dallas.Warren at monash.edu>wrote:

>   What forcefield is that for?  Sounds like it is more than likely one of
> the AMBER ones.****
>
> ** **
>
> What forcefield are you using for the rest of your system that you are
> simulating?****
>
> ** **
>
> Are they the same?  They should be.****
>
> ** **
>
> If not, are they compatible?  A minor number of them are compatible to some
> degree, such as with a version change for a given forcefield.  However, vast
> majority are not and combining those that aren’t compatible them will make a
> nice random number generator that you can spend lots of time using and not
> get anything out that is publishable.****
>
> ** **
>
> See http://www.gromacs.org/Documentation/Terminology/Force_Fields#Usageand the first point at
> http://www.gromacs.org/Documentation/How-tos/Parameterization ****
>
> ** **
>
> Catch ya,
>
> Dr. Dallas Warren****
>
> Medicinal Chemistry and Drug Action****
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at monash.edu****
>
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail. ****
>
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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
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E-mail : monu46010 at yahoo.com
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