Hi, I am looking at the file ffbonded.itp located in the oplsaa.ff directory (usually located in /usr/local/gromacs/share/gromacs/top/oplsaa.ff). I see the following entry in the [ dihedraltypes ] section:
C3 CT OH HO 3 0.41840 1.25520 0.00000 -1.67360 0.00000 0.00000 ; Alcohols with scl14 = 2,2 I have two questions about this entry: (1) What does the atom type "C3" represent? "CT" represents a tetrahedral carbon, "OH" represents an alcohol oxygen, and "HO" represents an alcohol hydrogen. But what does "C3" represent? The paper Cornell et al., J. Am. Chem. Soc. 1995, 117, 5179-5197 ( located at: http://pubs.acs.org/doi/abs/10.1021/ja00124a002 ) has a partial list of AMBER atom type abbreviations on page 5182, but I do not see C3 listed there. (2) What does the entry mean when it says "scl14 = 2,2"? Do you have any thoughts on this? Thank you so very much for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
