[gmx-users] N-Acetylglucosamine (NAG) in OPLS-AA
Ehud Schreiber
schreib at compugen.co.il
Tue Nov 15 10:38:23 CET 2011
Hi,
I am interested in the structure of a protein where some asparagine
residues are N-glycosylated by N-Acetylglucosamine (NAG). As a first
step I tried to model NAG itself (see e.g.
http://xray.bmc.uu.se/hicup/NAG/index.html) in the OPLS-AA force field
using implicit solvation; this has involved a surprisingly (for me)
large amount of tinkering. Here I'd like to present the changes I needed
to make to the oplsaa.ff/* force field files in order to accomplish
this; I would like to elicit comments, and hopefully this will also be
useful to others.
1) Added to aminoacids.rtp :
[ NAG ] ; N-Acetylglucosamine
[ atoms ]
C1 opls_195 +0.365 1
HC1 opls_196 +0.100 1
O1 opls_187 -0.700 1
HO1 opls_188 +0.435 1
C5 opls_183 +0.170 1
HC5 opls_185 +0.030 1
O5 opls_180 -0.400 1
C2 opls_229 +0.140 2
HC2 opls_140 +0.060 2
N2 opls_238 -0.500 2
HN2 opls_241 +0.300 2
C3 opls_158 +0.205 3
HC3 opls_140 +0.060 3
O3 opls_154 -0.683 3
HO3 opls_155 +0.418 3
C4 opls_158 +0.205 4
HC4 opls_140 +0.060 4
O4 opls_154 -0.683 4
HO4 opls_155 +0.418 4
C6 opls_157 +0.145 5
HC61 opls_140 +0.060 5
HC62 opls_140 +0.060 5
O6 opls_154 -0.683 5
HO6 opls_155 +0.418 5
C7 opls_235 +0.500 6
O7 opls_236 -0.500 6
C8 opls_135 -0.180 7
HC81 opls_140 +0.060 7
HC82 opls_140 +0.060 7
HC83 opls_140 +0.060 7
[ bonds ]
C1 HC1
C1 O1
C1 C2
C1 O5
O1 HO1
C2 HC2
C2 N2
C2 C3
N2 HN2
N2 C7
C3 HC3
C3 O3
C3 C4
O3 HO3
C4 HC4
C4 O4
C4 C5
O4 HO4
C5 HC5
C5 O5
C5 C6
C6 HC61
C6 HC62
C6 O6
O6 HO6
C7 O7
C7 C8
C8 HC81
C8 HC82
C8 HC83
2) Added to aminoacids.hdb :
NAG 12
1 5 HC1 C1 O5 O1 C2
1 5 HC2 C2 C1 N2 C3
1 5 HC3 C3 C2 O3 C4
1 5 HC4 C4 C3 O4 C5
1 5 HC5 C5 C4 C6 O5
1 2 HO1 O1 C1 C2
1 2 HO3 O3 C3 C4
1 2 HO4 O4 C4 C5
1 2 HO6 O6 C6 C5
1 1 HN2 N2 C2 C7
2 6 HC6 C6 C5 O6
3 4 HC8 C8 C7 N2
3) Added to ffbonded.itp :
[ angletypes ]
; i j k func th0 cth
CO CT N 1 109.700 669.440 ; copied from: CT CT
N ; ALA JACS 94, 2657
[ dihedraltypes ]
; i j k l func coefficients
HC CO OH HO 3 0.94140 2.82420 0.00000
-3.76560 0.00000 0.00000 ; copied from: HC CT OH HO ;
alcohols AA
CT CO OH HO 3 -0.44350 3.83255 0.72801
-4.11705 0.00000 0.00000 ; copied from: CT CT OH HO ;
alcohols AA
HC CO CT HC 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 ; copied from: HC CT CT HC ;
hydrocarbon *new* 11/99
HC CO CT N 3 0.97069 2.91206 0.00000
-3.88275 0.00000 0.00000 ; copied from: HC CT CT N ;
N-ethylformamide
HC CT CO OH 3 0.97905 2.93716 0.00000
-3.91622 0.00000 0.00000 ; copied from: HC CT CT OH ;
alcohols, ethers AA
C N CT CO 3 -4.70700 2.92044 1.78656
0.00000 0.00000 0.00000 ; copied from: C N CT CT ;
N-ethylformamide
N CT CT OH 3 9.89307 -4.71746 3.67774
-8.85335 0.00000 0.00000 ; copied from : N CT_2 CT OH ; Chi for Ser
& Thr
N CT CO OH 3 9.89307 -4.71746 3.67774
-8.85335 0.00000 0.00000 ; copied from : N CT_2 CT OH ; Chi for Ser
& Thr
N CT CO OS 3 2.92880 -1.46440 0.20920
-1.67360 0.00000 0.00000 ; copied from: N3 CT CT OS ;
Guess for lipids
4) Added to gbsa.itp :
opls_180 0.152 1 1.080 0.1535 0.85 ; copied from opls_154 ;
opls_183 0.18 1 1.276 0.190 0.72 ; copied from opls_158 ;
opls_185 0.1 1 1 0.125 0.85 ; copied from opls_140 ;
opls_187 0.152 1 1.080 0.1535 0.85 ; copied from opls_154 ;
opls_188 0.1 1 1 0.105 0.85 ; copied from opls_155 ;
opls_195 0.18 1 1.276 0.190 0.72 ; copied from opls_158 ;
opls_196 0.1 1 1 0.125 0.85 ; copied from opls_140 ;
opls_229 0.18 1 1.276 0.190 0.72 ; copied from opls_158 ;
So, are my choices reasonable? Could this have been done in some easier
fashion?
Thanks,
Ehud Schreiber.
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