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
--
========================================
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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