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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