Hello,<br><br>I first used Antechamber and Leap to generate the topology and coordinate files for benzamide.pdb.<br><br>I then converted them to gromacs formats and added the water molecules using the following commands:<br>
<br>editconf -f benz.gro -bt dodecahedron -d 1.2 -o benz_box.gro<br><br>genbox -cp benz_box.gro -cs tip4p.gro (there was no tip3p.gro) -p benz.top -o benz_solvated.gro<br><br><br><div id=":1py">*************************************************************<br>
; benz.top created by <a href="http://rdparm2gmx.pl/" target="_blank">rdparm2gmx.pl</a> Wed Jun 8 14:58:07 MDT 2011<br><br>[ defaults ]<br>; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br>1 2 yes 0.5 0.8333<br>
<br>[ atomtypes ]<br>;name bond_type mass charge ptype sigma epsilon<br>n n 0.0000 0.0000 A 3.25000e-01 7.11280e-01<br>c c 0.0000 0.0000 A 3.39967e-01 3.59824e-01<br>
ha ha 0.0000 0.0000 A 2.59964e-01 6.27600e-02<br>hn hn 0.0000 0.0000 A 1.06908e-01 6.56888e-02<br>ca ca 0.0000 0.0000 A 3.39967e-01 3.59824e-01<br>o o 0.0000 0.0000 A 2.95992e-01 8.78640e-01<br>
<br>[ moleculetype ]<br>; Name nrexcl<br>solute 3<br><br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass typeB chargeB<br> 1 ca 1 MOL C 1 -0.07700 12.000000<br>
2 ca 1 MOL C1 2 -0.13800 12.000000<br> 3 ca 1 MOL C2 3 -0.10900 12.000000<br> 4 ca 1 MOL C3 4 -0.13900 12.000000<br> 5 ca 1 MOL C4 5 -0.10500 12.000000<br>
6 ca 1 MOL C5 6 -0.14160 12.000000<br> 7 c 1 MOL C6 7 0.67070 12.000000<br> 8 o 1 MOL O 8 -0.61010 16.000000<br> 9 n 1 MOL N 9 -0.67400 14.000000<br>
10 ha 1 MOL H 10 0.15600 1.000000<br> 11 ha 1 MOL H1 11 0.13800 1.000000<br> 12 ha 1 MOL H2 12 0.13500 1.000000<br> 13 ha 1 MOL H3 13 0.13600 1.000000<br>
14 ha 1 MOL H4 14 0.13300 1.000000<br> 15 hn 1 MOL H5 15 0.31750 1.000000<br> 16 hn 1 MOL H6 16 0.30750 1.000000<br><br>[ bonds ]<br>
; ai aj funct r k<br> 1 10 1 1.0870e-01 2.8811e+05<br> 2 11 1 1.0870e-01 2.8811e+05<br> 3 12 1 1.0870e-01 2.8811e+05<br> 4 13 1 1.0870e-01 2.8811e+05<br> 5 14 1 1.0870e-01 2.8811e+05<br>
9 15 1 1.0090e-01 3.4326e+05<br> 9 16 1 1.0090e-01 3.4326e+05<br> 1 2 1 1.3870e-01 4.0033e+05<br> 1 6 1 1.3870e-01 4.0033e+05<br> 2 3 1 1.3870e-01 4.0033e+05<br>
3 4 1 1.3870e-01 4.0033e+05<br> 4 5 1 1.3870e-01 4.0033e+05<br> 5 6 1 1.3870e-01 4.0033e+05<br> 6 7 1 1.4870e-01 2.9263e+05<br> 7 8 1 1.2140e-01 5.4225e+05<br>
7 9 1 1.3450e-01 4.0016e+05<br><br>[ pairs ]<br>; ai aj funct<br> 1 12 1<br> 1 14 1<br> 2 13 1<br> 10 3 1<br> 3 14 1<br> 4 11 1<br>
5 12 1<br> 10 5 1<br> 6 11 1<br> 6 13 1<br> 6 15 1<br> 6 16 1<br> 10 7 1<br> 7 14 1<br> 8 15 1<br> 8 16 1<br>
10 11 1<br> 11 12 1<br> 12 13 1<br> 13 14 1<br> 1 4 1<br> 1 8 1<br> 1 9 1<br> 2 5 1<br> 2 7 1<br> 6 3 1<br>
4 7 1<br> 5 8 1<br> 5 9 1<br><br>[ angles ]<br>; ai aj ak funct theta cth<br> 1 2 11 1 1.2001e+02 4.0551e+02<br> 2 1 10 1 1.2001e+02 4.0551e+02<br>
2 3 12 1 1.2001e+02 4.0551e+02<br> 3 2 11 1 1.2001e+02 4.0551e+02<br> 3 4 13 1 1.2001e+02 4.0551e+02<br> 4 3 12 1 1.2001e+02 4.0551e+02<br> 4 5 14 1 1.2001e+02 4.0551e+02<br>
5 4 13 1 1.2001e+02 4.0551e+02<br> 6 1 10 1 1.2001e+02 4.0551e+02<br> 6 5 14 1 1.2001e+02 4.0551e+02<br> 7 9 15 1 1.1846e+02 4.1179e+02<br> 7 9 16 1 1.1846e+02 4.1179e+02<br>
15 9 16 1 1.1785e+02 3.3246e+02<br> 1 2 3 1 1.1997e+02 5.6216e+02<br> 1 6 5 1 1.1997e+02 5.6216e+02<br> 1 6 7 1 1.2014e+02 5.4091e+02<br> 2 1 6 1 1.1997e+02 5.6216e+02<br>
2 3 4 1 1.1997e+02 5.6216e+02<br> 3 4 5 1 1.1997e+02 5.6216e+02<br> 4 5 6 1 1.1997e+02 5.6216e+02<br> 5 6 7 1 1.2014e+02 5.4091e+02<br> 6 7 8 1 1.2344e+02 5.7463e+02<br>
6 7 9 1 1.1514e+02 5.7296e+02<br> 8 7 9 1 1.2203e+02 6.3455e+02<br><br>[ dihedrals ]<br>;i j k l func C0 ... C5<br> 1 2 3 12 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br>
1 6 5 14 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br> 2 3 4 13 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br> 10 1 2 3 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br>
3 4 5 14 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br> 4 3 2 11 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br> 5 4 3 12 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br>
10 1 6 5 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br> 6 1 2 11 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br> 6 5 4 13 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br>
6 7 9 15 3 20.92000 0.00000 -20.92000 0.00000 0.00000 0.00000 ;<br> 6 7 9 16 3 20.92000 0.00000 -20.92000 0.00000 0.00000 0.00000 ;<br> 10 1 6 7 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br>
7 6 5 14 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br> 8 7 9 15 3 29.28800 -8.36800 -20.92000 0.00000 0.00000 0.00000 ;<br> 8 7 9 16 3 29.28800 -8.36800 -20.92000 0.00000 0.00000 0.00000 ;<br>
10 1 2 11 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br> 11 2 3 12 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br> 12 3 4 13 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br>
13 4 5 14 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br> 10 1 6 2 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;<br> 1 3 2 11 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;<br>
2 4 3 12 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;<br> 3 5 4 13 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;<br> 4 6 5 14 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;<br>
7 15 9 16 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;<br> 1 2 3 4 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br> 1 6 5 4 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br>
1 6 7 8 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br> 1 6 7 9 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br> 2 1 6 5 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br>
2 1 6 7 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br> 2 3 4 5 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br> 6 1 2 3 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br>
3 4 5 6 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br> 4 5 6 7 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br> 5 6 7 8 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br>
5 6 7 9 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;<br> 6 9 7 8 3 87.86400 0.00000 -87.86400 0.00000 0.00000 0.00000 ;<br><br>
<br>
[ system ]<br>16 system in water<br><br>[ molecules ]<br>; Compound nmols<br>solute 1<br>SOL 697<br><br><br>*******************************************************************************************<br>
<br><br>When I try to run the minimizer, I get this error:<br><br>Fatal error:<br>No such moleculetype SOL<br><br>****************************************************************<br><br>I added this line to benz.top file:<br>
<br><font size="2"><b>#include "amber99.ff/tip4p.itp"</b></font><br><br>[ system ]<br>16 system in water<br><br>I get this error when minimizing:<br><br>Fatal error:<br>Atomtype OW_tip4p not found<br><br>Thanks<br>
Massih<br></div>