Hi
I have a few questions on GAFFLipid parameters.
In GAFFlipid the nonbonding parameters have been readjusted, requiring the dihedral parameters to also be readjusted.
I see the new parameters in the GAFFlipid.frcmod file downloaded from lipidbook.
Here's what I don't understand.
>From the traditional gaff.dat (Version 1.4, March 2010) The following dihedral parameters are listed
X -c -c3-X 6 0.000 180.000 2.000 JCC, 7, (1986), 230
hc-c3-c -o 1 0.80 0.0 -1. Junmei et al, 1999
hc-c3-c -o 1 0.08 180.0 3. Junmei et al, 1999
>From GAFFlipid.frcmod the following are listed
o -c -a3-hl 1 0.000 180.000 2.000 same as X -c -c3-X
o -c -a3-a3 1 0.000 180.000 2.000 same as X -c -c3-X
So are the GAFFlipid LJ parameters accounting for this difference?
Also are there any systems investigated that have the connection c-os-c3-c3 investigated with lipid parameters so far?
Thanks
Cody
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 17 2013 - 12:00:03 PDT
