<DIV>Hi Alan , Oliver</DIV>
<DIV> I have obtained the gromacs format files by amb2gmx.pl script, but I am not sure if this flies are correct<SPAN style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; BORDER-COLLAPSE: separate; FONT: medium Simsun; WHITE-SPACE: normal; ORPHANS: 2; LETTER-SPACING: normal; COLOR: rgb(0,0,0); WORD-SPACING: 0px; -webkit-text-size-adjust: auto; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px" class="Apple-style-span"><SPAN style="LINE-HEIGHT: 18px; FONT-FAMILY: verdana, ËÎÌå; COLOR: rgb(73,73,73); FONT-SIZE: 12px" class="Apple-style-span"><SPAN class="Apple-converted-space"> ,</SPAN></SPAN></SPAN><BR>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. </DIV>
<DIV> Would you give me some advice? Thank your very much.</DIV>
<DIV> </DIV>
<DIV>all the best</DIV>
<DIV>xiaodu </DIV>
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<DIV>; lambda.top created by rdparm2gmx.pl Fri Dec 24 10:22:31 CST 2010</DIV>
<DIV>[ defaults ]<BR>; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<BR>1 2 yes 0.5 0.8333</DIV>
<DIV>[ atomtypes ]<BR>;name bond_type mass charge ptype sigma epsilon<BR>HO HO 0.0000 0.0000 A 0.00000e+00 0.00000e+00<BR>H1 H1 0.0000 0.0000 A 2.47135e-01 6.56888e-02<BR>OS OS 0.0000 0.0000 A 3.00001e-01 7.11280e-01<BR>CG CG 0.0000 0.0000 A 3.39967e-01 4.57730e-01<BR>H2 H2 0.0000 0.0000 A 2.29317e-01 6.56888e-02<BR>OH OH 0.0000 0.0000 A 3.06647e-01 8.80314e-01</DIV>
<DIV>[ moleculetype ]<BR>; Name nrexcl<BR>solute 3</DIV>
<DIV>[ atoms ]<BR>; nr type resnr residue atom cgnr charge mass typeB chargeB<BR> 1 HO 1 ROH HO1 1 0.44500 1.000000<BR> 2 OH 1 ROH O1 2 -0.63900 16.000000<BR> 3 CG 2 4GA C1 3 0.50900 12.000000<BR> 4 H2 2 4GA H1 4 0.00000 1.000000<BR> 5 CG 2 4GA C2 5 0.24600 12.000000<BR> 6 H1 2 4GA H2 6 0.00000 1.000000<BR> 7 OH 2 4GA O2 7 -0.71300 16.000000<BR> 8 HO 2 4GA H2O 8 0.43700 1.000000<BR> 9 CG 2 4GA C3 9 0.28600 12.000000<BR> 10 H1 2 4GA H3 10 0.00000 1.000000<BR> 11 OH 2 4GA O3 11 -0.69900 16.000000<BR> 12 HO 2 4GA H3O 12 0.42700 1.000000<BR> 13 CG 2 4GA C4 13 0.25400 12.000000<BR> 14 H1 2 4GA H4 14 0.00000 1.000000<BR> 15 CG 2 4GA C5 15 0.28300 12.000000<BR> 16 H1 2 4GA H5 16 0.00000 1.000000<BR> 17 OS 2 4GA O5 17 -0.57400 16.000000<BR> 18 CG 2 4GA C6 18 0.27600 12.000000<BR> 19 H1 2 4GA H61 19 0.00000 1.000000<BR> 20 H1 2 4GA H62 20 0.00000 1.000000<BR> 21 OH 2 4GA O6 21 -0.68200 16.000000<BR> 22 HO 2 4GA H6O 22 0.41800 1.000000<BR> 23 OS 2 4GA O4 23 -0.46800 16.000000<BR> 24 CG 3 0GA C1 24 0.50900 12.000000<BR> 25 H2 3 0GA H1 25 0.00000 1.000000<BR> 26 CG 3 0GA C2 26 0.24600 12.000000<BR> 27 H1 3 0GA H2 27 0.00000 1.000000<BR> 28 OH 3 0GA O2 28 -0.71300 16.000000<BR> 29 HO 3 0GA H2O 29 0.43700 1.000000<BR> 30 CG 3 0GA C3 30 0.28600 12.000000<BR> 31 H1 3 0GA H3 31 0.00000 1.000000<BR> 32 OH 3 0GA O3 32 -0.69900 16.000000<BR> 33 HO 3 0GA H3O 33 0.42700 1.000000<BR> 34 CG 3 0GA C4 34 0.25400 12.000000<BR> 35 H1 3 0GA H4 35 0.00000 1.000000<BR> 36 OH 3 0GA O4 36 -0.71000 16.000000<BR> 37 HO 3 0GA H4O 37 0.43600 1.000000<BR> 38 CG 3 0GA C5 38 0.28300 12.000000<BR> 39 H1 3 0GA H5 39 0.00000 1.000000<BR> 40 OS 3 0GA O5 40 -0.57400 16.000000<BR> 41 CG 3 0GA C6 41 0.27600 12.000000<BR> 42 H1 3 0GA H61 42 0.00000 1.000000<BR> 43 H1 3 0GA H62 43 0.00000 1.000000<BR> 44 OH 3 0GA O6 44 -0.68200 16.000000<BR> 45 HO 3 0GA H6O 45 0.41800 1.000000</DIV>
<DIV>[ bonds ]<BR>; ai aj funct r k<BR> 1 2 1 9.6000e-02 4.6275e+05<BR> 21 22 1 9.6000e-02 4.6275e+05<BR> 18 19 1 1.0900e-01 2.8451e+05<BR> 18 20 1 1.0900e-01 2.8451e+05<BR> 15 16 1 1.0900e-01 2.8451e+05<BR>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</DIV>
<DIV>[ pairs ]<BR>; ai aj funct<BR> 2 6 1<BR> 1 4 1<BR> 1 5 1<BR> 1 17 1</DIV>
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<DIV> 5 23 1<BR> 3 11 1<BR> 3 13 1<BR> 3 18 1<BR> 40 44 1<BR> 36 40 1<BR> 36 41 1<BR> 34 44 1<BR> 32 36 1<BR> 32 38 1<BR> 30 40 1<BR> 30 41 1<BR> 28 40 1<BR> 28 32 1<BR> 28 34 1<BR> 26 38 1<BR> 26 36 1<BR> 24 32 1<BR> 24 34 1<BR> 24 41 1</DIV>
<DIV>[ angles ]<BR>; ai aj ak funct theta cth<BR> 2 3 4 1 1.1000e+02 5.0208e+02<BR> 1 2 3 1 1.0950e+02 4.6024e+02<BR> 23 24 25 1 1.1000e+02 5.0208e+02<BR> 20 18 21 1 1.1000e+02 5.0208e+02<BR> 19 18 20 1 1.0950e+02 3.7656e+02<BR>~~~~~~~~~~~~~~~~~~~</DIV>
<DIV>[ dihedrals ]<BR>;i j k l func C0 ... C5<BR> 2 3 5 6 3 0.20920 0.62760 0.00000 -0.83680 0.00000 0.00000 ;<BR> 1 2 3 4 3 0.75312 2.25936 0.00000 -3.01248 0.00000 0.00000 ;<BR> 1 2 3 5 3 0.75312 2.25936 0.00000 -3.01248 0.00000 0.00000 ;<BR>~~~~~~~~~~~~~~~~~<BR>[ system ]<BR>45 system</DIV>
<DIV>[ molecules ]<BR>; Compound nmols<BR>solute 1<BR>-------------------------------------------------------------------------------------------------</DIV>
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