[gmx-users] Re:gmx-users Digest, Vol 80, Issue 164
gromacs564
gromacs564 at 126.com
Sat Dec 25 11:13:03 CET 2010
Hi Alan , Oliver
I have obtained the gromacs format files by amb2gmx.pl script, but I am not sure if this flies are correct ,
because all of the [pairs](1-4 interaction) are zero in gromacs top files. I don't know whether this files are correct or not.
Would you give me some advice? Thank your very much.
all the best
xiaodu
------------------------------------------------------------------------------------------------
-------------------------------------------------------------------------------------------------
; lambda.top created by rdparm2gmx.pl Fri Dec 24 10:22:31 CST 2010
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon
HO HO 0.0000 0.0000 A 0.00000e+00 0.00000e+00
H1 H1 0.0000 0.0000 A 2.47135e-01 6.56888e-02
OS OS 0.0000 0.0000 A 3.00001e-01 7.11280e-01
CG CG 0.0000 0.0000 A 3.39967e-01 4.57730e-01
H2 H2 0.0000 0.0000 A 2.29317e-01 6.56888e-02
OH OH 0.0000 0.0000 A 3.06647e-01 8.80314e-01
[ moleculetype ]
; Name nrexcl
solute 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB
1 HO 1 ROH HO1 1 0.44500 1.000000
2 OH 1 ROH O1 2 -0.63900 16.000000
3 CG 2 4GA C1 3 0.50900 12.000000
4 H2 2 4GA H1 4 0.00000 1.000000
5 CG 2 4GA C2 5 0.24600 12.000000
6 H1 2 4GA H2 6 0.00000 1.000000
7 OH 2 4GA O2 7 -0.71300 16.000000
8 HO 2 4GA H2O 8 0.43700 1.000000
9 CG 2 4GA C3 9 0.28600 12.000000
10 H1 2 4GA H3 10 0.00000 1.000000
11 OH 2 4GA O3 11 -0.69900 16.000000
12 HO 2 4GA H3O 12 0.42700 1.000000
13 CG 2 4GA C4 13 0.25400 12.000000
14 H1 2 4GA H4 14 0.00000 1.000000
15 CG 2 4GA C5 15 0.28300 12.000000
16 H1 2 4GA H5 16 0.00000 1.000000
17 OS 2 4GA O5 17 -0.57400 16.000000
18 CG 2 4GA C6 18 0.27600 12.000000
19 H1 2 4GA H61 19 0.00000 1.000000
20 H1 2 4GA H62 20 0.00000 1.000000
21 OH 2 4GA O6 21 -0.68200 16.000000
22 HO 2 4GA H6O 22 0.41800 1.000000
23 OS 2 4GA O4 23 -0.46800 16.000000
24 CG 3 0GA C1 24 0.50900 12.000000
25 H2 3 0GA H1 25 0.00000 1.000000
26 CG 3 0GA C2 26 0.24600 12.000000
27 H1 3 0GA H2 27 0.00000 1.000000
28 OH 3 0GA O2 28 -0.71300 16.000000
29 HO 3 0GA H2O 29 0.43700 1.000000
30 CG 3 0GA C3 30 0.28600 12.000000
31 H1 3 0GA H3 31 0.00000 1.000000
32 OH 3 0GA O3 32 -0.69900 16.000000
33 HO 3 0GA H3O 33 0.42700 1.000000
34 CG 3 0GA C4 34 0.25400 12.000000
35 H1 3 0GA H4 35 0.00000 1.000000
36 OH 3 0GA O4 36 -0.71000 16.000000
37 HO 3 0GA H4O 37 0.43600 1.000000
38 CG 3 0GA C5 38 0.28300 12.000000
39 H1 3 0GA H5 39 0.00000 1.000000
40 OS 3 0GA O5 40 -0.57400 16.000000
41 CG 3 0GA C6 41 0.27600 12.000000
42 H1 3 0GA H61 42 0.00000 1.000000
43 H1 3 0GA H62 43 0.00000 1.000000
44 OH 3 0GA O6 44 -0.68200 16.000000
45 HO 3 0GA H6O 45 0.41800 1.000000
[ bonds ]
; ai aj funct r k
1 2 1 9.6000e-02 4.6275e+05
21 22 1 9.6000e-02 4.6275e+05
18 19 1 1.0900e-01 2.8451e+05
18 20 1 1.0900e-01 2.8451e+05
15 16 1 1.0900e-01 2.8451e+05
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ pairs ]
; ai aj funct
2 6 1
1 4 1
1 5 1
1 17 1
~~~~~~~~~~~~~~~~~~~~
5 23 1
3 11 1
3 13 1
3 18 1
40 44 1
36 40 1
36 41 1
34 44 1
32 36 1
32 38 1
30 40 1
30 41 1
28 40 1
28 32 1
28 34 1
26 38 1
26 36 1
24 32 1
24 34 1
24 41 1
[ angles ]
; ai aj ak funct theta cth
2 3 4 1 1.1000e+02 5.0208e+02
1 2 3 1 1.0950e+02 4.6024e+02
23 24 25 1 1.1000e+02 5.0208e+02
20 18 21 1 1.1000e+02 5.0208e+02
19 18 20 1 1.0950e+02 3.7656e+02
~~~~~~~~~~~~~~~~~~~
[ dihedrals ]
;i j k l func C0 ... C5
2 3 5 6 3 0.20920 0.62760 0.00000 -0.83680 0.00000 0.00000 ;
1 2 3 4 3 0.75312 2.25936 0.00000 -3.01248 0.00000 0.00000 ;
1 2 3 5 3 0.75312 2.25936 0.00000 -3.01248 0.00000 0.00000 ;
~~~~~~~~~~~~~~~~~
[ system ]
45 system
[ molecules ]
; Compound nmols
solute 1
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