Hello, it was discussed at times how to parametrize N-terminal neutral
amino acid residue (see for example:
http://archive.ambermd.org/200606/0104.html ). R.E.DD.B contributors of
N-terminal neutral residue fragments (for example, project F-15) provide
script to convert mol2 file to Amber OFF library. But I was confused to
notice that they set atom type N3 (sp3 N for charged amino groups) to
N-terminal nitrogen. There are no impropers in parm99.dat for N3 to keep it
planar, while I think that in concept of MM Amber force field neutral
aminigroup should be strictly sp2. So what is the reason of N3 choice?
Here is an important part of script for NH2-terminal fragment of
dimethylalanine N0AI:
N0AI = loadmol2 N0AI.mol2
set N0AI name "N0AI"
# head = null
set N0AI tail N0AI.1.C
set N0AI.1 connect0 N0AI.1.N
set N0AI.1 connect1 N0AI.1.C
set N0AI.1 restype protein
set N0AI.1 name "N0AI"
# set FF atom types
set N0AI.1.N type N3
set N0AI.1.H1 type H
set N0AI.1.H2 type H
set N0AI.1.C type C
set N0AI.1.O type O
set N0AI.1.CA type CT
set N0AI.1.CB1 type CT
set N0AI.1.HB11 type HC
set N0AI.1.HB12 type HC
set N0AI.1.HB13 type HC
set N0AI.1.CB2 type CT
set N0AI.1.HB21 type HC
set N0AI.1.HB22 type HC
set N0AI.1.HB23 type HC
# save the OFF library
saveoff N0AI N0AI.off
Thanks a lot!
--
Dmitry Nilov,
Lomonosov Moscow State University
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Received on Wed Mar 31 2010 - 04:00:02 PDT
