Dear All:
I am using OPLS force field (OPLS FF) to do molecular dynamics
simulations. My system contains DPPC lipid, protein and a small
molecule. I have the following questions:
1, where can I get the topology files for the DPPC lipids?
2, How to prepare the topology files for the small molecules? I plan
to calculate the charges of each atoms by QM method.After I got the
charges and atom radius, how to prepare the topology files?
3, I am using GROMACS 3 and I found there are three all-atom force
fields there:
----------------------------------------------
0: GROMOS96 43a1 force field
1: GROMOS96 43b1 vacuum force field
2: GROMOS96 43a2 force field (improved alkane dihedrals)
3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
7: Encad all-atom force field, using scaled-down vacuum charges
8: Encad all-atom force field, using full solvent charges
-------------------------------------------------
among them, 6, 7, and 8 are all-atom force fields, right? My question
is are 7 and 8 also OPLS force fields? If so, which one is
recommendated to use in lipid-protein complex systems MD simulations?
What are the differences between 6, 7 and 8.
Sincerely Yours
Ruo-Xu Gu
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