On Wed, Nov 14, 2012, FyD wrote:
>
> About the LYN residue many (but not all) of the
> amber??/dat/leap/lib/*_amino*.lib files
>
> My understanding is that the atom type of NZ should be NT (& not N3)
> and the atom types of the 2 hydrogen atoms of CE should be H1 (& not
> HP). See below...
>
> Could you tell me if this problem is known? thank you.
>
> regards, Francois
>
>
> !entry.LYN.unit.atoms table str name str type int typex int resx
> int flags int seq int elmnt dbl chg
> [...]
> "CE" "CT" 0 1 131072 14 6 0.326040
> "HE2" "HP" 0 1 131072 15 1 -0.033580 ! error
> "HE3" "HP" 0 1 131072 16 1 -0.033580 ! error
> "NZ" "N3" 0 1 131072 17 7 -1.035810 ! error
> "HZ2" "H" 0 1 131072 18 1 0.386040
> "HZ3" "H" 0 1 131072 19 1 0.386040
>
> ->
> !entry.LYN.unit.atoms table str name str type int typex int resx
> int flags int seq int elmnt dbl chg
> [...]
> "CE" "CT" 0 1 131072 14 6 0.326040
> "HE2" "H1" 0 1 131072 15 1 -0.033580
> "HE3" "H1" 0 1 131072 16 1 -0.033580
> "NZ" "NT" 0 1 131072 17 7 -1.035810
> "HZ2" "H" 0 1 131072 18 1 0.386040
> "HZ3" "H" 0 1 131072 19 1 0.386040
>
I agree that your proposed changes make sense. It's only easy to fix atom
types when we go forward to a new force field, otherwise it becomes ambiguous
what is meant by "ff10" or "ff12SB". Jason may have thoughts here, but we'll
plan to get this change propagated into future force fields.
...thanks...dac
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Received on Mon Nov 26 2012 - 05:30:02 PST
