7 and 8 have nothing to do with OPLS-AA.
As the text tells you, it is the Encad forcefield
(http://www.sklogwiki.org/SklogWiki/index.php/ENCAD_%28force_field%29)
So that then leaves you with the OPLS-AA for you to use :-)
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of mirc...@sjtu.edu.cn
> Sent: Tuesday, 22 February 2011 4:18 PM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] membrane bilayer simulation by OPLS FF
>
> 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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