On 2/27/13 12:25 PM, 라지브간디 wrote:
Dear Justin,
I have looked over the chapter 5 and had difficult to understand the
interpreting the LJ 6-12 value for my ligand file.
I just want to give particular value only for NO ligand, therefore i want to
know how do i give them in topology file?
As you already mentioned that I should change them in [atomtypes] else special
interaction in [nonbond_params] in ffnonboneded.itp file. If i do that, I
wonder it could be giving this value for my protein too?
What i want in here is, how do i specify the value only for NO ligand in .itp
file which is created by pdb2gmx. I believe, the [pairs] column in the .itp
also only for 1-4 LJ value?
What you need to be clear about is that your NO molecule does not have LJ
parameters, but its constituent atoms do. Those parameters affect the way it
behaves, and if the atom types are the same as those used in protein groups,
then you would also be manipulating protein-protein and protein-NO interactions.
The best strategy, if you are attempting to only affect protein-NO, NO-NO,
and/or NO-solvent interactions is to define special [atomtypes] that are used
for the NO molecule that have C6/C12 parameters that give rise to the desired LJ
interactions. Anything listed in [atomtypes] will be used to calculate LJ
interactions according to standard combination rules. If you want some
magnitude of interaction that is not a result of the standard combination rules,
you need to define [nonbond_params] that will override combination rule values.
If you need further help, you will need to provide the ligand topology and
describe exactly the manner in which you need to modify it, otherwise all anyone
will end up doing is repeating the manual back to you :)
-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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