Dear Sir/Madam,<br><br>I have tried to creat the gro and top file for acid hexanoic by using the PRODRG server. However, the atom H in -COOH group could not be found and two O atoms are the same. <br clear="all"><br><span style="color: rgb(153, 51, 153);">[ moleculetype ]</span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);">; Name nrexcl</span><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);">DRG 3</span><br style="color: rgb(153, 51, 153);"><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);">[ atoms ]</span><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);">; nr type resnr resid atom cgnr charge mass</span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);"> 1 OM 1 DRG OAB 1 -0.767 15.9994 </span><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);"> 2 C 1 DRG CAI 1 0.343 12.0110 </span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);"> 3 OM 1 DRG OAC 1 -0.766 15.9994 </span><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);"> 4 CH2 1 DRG CAH 1 0.048 14.0270 </span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);"> 5 CH2 1 DRG CAG 1 0.047 14.0270 </span><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);"> 6 CH2 1 DRG CAF 1 0.047 14.0270 </span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);"> 7 CH2 1 DRG CAE 1 0.048 14.0270 </span><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);"> 8 CH2 1 DRG CAD 2 0.000 14.0270 </span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);"> 9 CH3 1 DRG CAA 3 0.000 15.0350 </span><br style="color: rgb(153, 51, 153);"><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);">[ bonds ]</span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);">; ai aj fu c0, c1, ...</span><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);"> 2 1 2 0.125 13400000.0 0.125 13400000.0 ; CAI OAB </span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);"> 2 3 2 0.125 13400000.0 0.125 13400000.0 ; CAI OAC </span><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);"> 2 4 2 0.153 7150000.0 0.153 7150000.0 ; CAI CAH </span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);"> 4 5 2 0.153 7150000.0 0.153 7150000.0 ; CAH CAG </span><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);"> 5 6 2 0.153 7150000.0 0.153 7150000.0 ; CAG CAF </span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);"> 6 7 2 0.153 7150000.0 0.153 7150000.0 ; CAF CAE </span><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);"> 7 8 2 0.153 7150000.0 0.153 7150000.0 ; CAE CAD </span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);"> 8 9 2 0.153 7150000.0 0.153 7150000.0 ; CAD CAA </span><br style="color: rgb(153, 51, 153);"><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);">[ pairs ]</span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);">; ai aj fu c0, c1, ...</span><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);"> 1 5 1 ; OAB CAG </span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);"> 2 6 1 ; CAI CAF </span><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);"> 3 5 1 ; OAC CAG </span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);"> 4 7 1 ; CAH CAE </span><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);"> 5 8 1 ; CAG CAD </span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);"> 6 9 1 ; CAF CAA </span><br style="color: rgb(153, 51, 153);"><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);">[ angles ]</span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);">; ai aj ak fu c0, c1, ...</span><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);"> 1 2 3 2 126.0 770.0 126.0 770.0 ; OAB CAI OAC </span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);"> 1 2 4 2 117.0 635.0 117.0 635.0 ; OAB CAI CAH </span><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);"> 3 2 4 2 117.0 635.0 117.0 635.0 ; OAC CAI CAH </span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);"> 2 4 5 2 109.5 520.0 109.5 520.0 ; CAI CAH CAG </span><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);"> 4 5 6 2 109.5 520.0 109.5 520.0 ; CAH CAG CAF </span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);"> 5 6 7 2 109.5 520.0 109.5 520.0 ; CAG CAF CAE </span><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);"> 6 7 8 2 109.5 520.0 109.5 520.0 ; CAF CAE CAD </span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);"> 7 8 9 2 109.5 520.0 109.5 520.0 ; CAE CAD CAA </span><br style="color: rgb(153, 51, 153);"><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);">[ dihedrals ]</span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);">; ai aj ak al fu c0, c1, m, ...</span><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);"> 2 1 3 4 2 0.0 167.4 0.0 167.4 ; imp CAI OAB OAC CAH </span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);"> 5 4 2 1 1 0.0 1.0 6 0.0 1.0 6 ; dih CAG CAH CAI OAB </span><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);"> 6 5 4 2 1 0.0 5.9 3 0.0 5.9 3 ; dih CAF CAG CAH CAI </span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);"> 7 6 5 4 1 0.0 5.9 3 0.0 5.9 3 ; dih CAE CAF CAG CAH </span><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);"> 8 7 6 5 1 0.0 5.9 3 0.0 5.9 3 ; dih CAD CAE CAF CAG </span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);"> 9 8 7 6 1 0.0 5.9 3 0.0 5.9 3 ; dih CAA CAD CAE CAF </span><br><br><br>Please help me to correct this mistake.<br>Many thanks.<br><br>Best regards,<br>
<br><br><br><div>Nguyen Van Cuong</div>
<div>PhD student - Curtin University of Technology</div>
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