On 3/22/13 3:14 PM, 라지브간디 wrote:
Dear Justin,
Actually I've manually added the heme -ligand parameters details such as bond,
angle and dihedral to my topology created by pdb2gmx via gromos43a1. ( Those
manually added parameters details are taken from charmm and amber ff, which are
available in some published articles ).
If you're doing this, you're creating a hybrid force field that makes no sense.
There are parameters for heme within Gromos96 already; why are you making
these modifications?
I confused while interpreting the improper values from those published article
where they both shown (amber and charmm) improper in X (generic indicator) way,
whereas the gromos improper values for atoms are in direct way by not using X
generic indicator.
Is that improper details are important for heme-ligand case ? If so, how do I
make them favor to gromos by this article values ?
Different force fields derive and implement parameters in different ways. Hence
why it makes no sense to try to combine them.
-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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