Dear all,
I noticed that in amino14ipq.lib (distributed with AmberTools14), the
charges of the CYM residue (deprotonated CYS, so formal charge -1) are the
same as for CYX, i.e. the overall net charge is zero:
!entry.CYM.unit.atoms table str name str type int typex int resx int
flags int seq int elmnt dbl chg
"N" "N" 0 1 131072 1 7 -0.49998
"H" "H" 0 1 131072 2 1 0.31825
"CA" "CX" 0 1 131072 3 6 0.02802
"HA" "H1" 0 1 131072 4 1 0.08954
"CB" "CT" 0 1 131072 5 6 -0.03151
"HB3" "H1" 0 1 131072 6 1 0.07734
"HB2" "H1" 0 1 131072 7 1 0.07734
"SG" "SH" 0 1 131072 8 16 -0.11357
"C" "C" 0 1 131072 9 6 0.61779
"O" "OD" 0 1 131072 10 8 -0.56322
compare with CYX:
!entry.CYX.unit.atoms table str name str type int typex int resx int
flags int seq int elmnt dbl chg
"N" "N" 0 1 131072 1 7 -0.49998
"H" "H" 0 1 131072 2 1 0.31825
"CA" "CX" 0 1 131072 3 6 0.02802
"HA" "H1" 0 1 131072 4 1 0.08954
"CB" "2C" 0 1 131072 5 6 -0.03151
"HB2" "H1" 0 1 131072 6 1 0.07734
"HB3" "H1" 0 1 131072 7 1 0.07734
"SG" "S" 0 1 131072 8 16 -0.11357
"C" "C" 0 1 131072 9 6 0.61779
"O" "OD" 0 1 131072 10 8 -0.56322
I just happened on this by chance - I have no intention to use ff14ipq
(esp. with CYM) in the near future, but if this is an error, I'm sure it is
worth fixing!
Best,
Marc
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Received on Thu Jul 24 2014 - 05:30:03 PDT
