[gmx-users] ATP/ADP+Pi

[Justin Lemkul]

On 10/26/12 11:12 AM, 闪耀星空 wrote:
> GMX-users: I am working with ATP+protein and ADP+Pi+protein  in gromos43a1.ff
> force field,but I  find only ATP parameters in the  aminoacids.rtp file
> .Where can I  achieve the ADP+Pi parameters ???  I  wanted use the parameters
> from((http://www.pharmacy.manchester.ac.uk/bryce/amber)  )   but it seemed

These parameters are for use with an AMBER force field, so indeed they are not 
appropriate for combining with Gromos96 43A1.

You either need to choose a force field that already describes the species of 
interest (AMBER seems to be a reasonable choice), or you need to derive 
parameters for anything that's missing yourself (not an easy task).

http://www.gromacs.org/Documentation/How-tos/Parameterization

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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