<br><span class="gmail_quote"></span><span style="color: rgb(51, 102, 255);">Dear all,</span><br style="color: rgb(51, 102, 255);"><br style="color: rgb(51, 102, 255);"><span style="color: rgb(51, 102, 255);">I have a problem in the generation of the topology file of a ligand
</span><br style="color: rgb(51, 102, 255);"><span style="color: rgb(51, 102, 255);">using x2top program. I think that it's a problem with</span><br style="color: rgb(51, 102, 255);"><span style="color: rgb(51, 102, 255);">
the detection of the connectivity by the program.I am</span><br style="color: rgb(51, 102, 255);"><span style="color: rgb(51, 102, 255);">using the version 3.3.2 of Gromacs.</span><br style="color: rgb(51, 102, 255);"><br style="color: rgb(51, 102, 255);">
<span style="color: rgb(51, 102, 255);">As an example i have take only a fragment of my molecule,</span><br style="color: rgb(51, 102, 255);"><span style="color: rgb(51, 102, 255);">that it's a benzamidine group.</span>
<br><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">ATOM 1 C ABK 0 -1.230 -1.842 0.078 C</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">
ATOM 2 C ABK 0 -0.039 0.308 0.150 C</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">ATOM 3 C ABK 0 0.010 -2.531 0.093 C
</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">ATOM 4 C ABK 0 1.225 -1.801 0.134 C</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">
ATOM 5 C ABK 0 1.200 -0.384 0.164 C</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">ATOM 6 C ABK 0 -0.046 2.022 0.175 C
</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">ATOM 7 C ABK 0 -1.254 -0.424 0.102 C</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">
ATOM 8 H ABK 0 -2.193 -2.420 0.045 H</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">ATOM 9 H ABK 0 0.029 -3.654 0.071 H
</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">ATOM 10 H ABK 0 -1.494 2.171 1.516 H</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">
ATOM 11 H ABK 0 -0.807 3.690 0.913 H</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">ATOM 12 H ABK 0 1.997 2.551 -0.694 H
</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">ATOM 13 H ABK 0 0.660 3.385 -1.519 H</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">
ATOM 14 H ABK 0 2.163 0.193 0.197 H</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">ATOM 15 H ABK 0 2.208 -2.346 0.142 H
</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">ATOM 16 H ABK 0 -2.237 0.119 0.084 H</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">
ATOM 17 N ABK 0 -0.826 2.661 0.908 N</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">ATOM 18 N ABK 0 0.999 2.793 -0.751 N
</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">CONECT 7 1 2 16</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">CONECT 1 7 3 8</span><br style="color: rgb(0, 0, 0);">
<span style="color: rgb(0, 0, 0);">CONECT 2 7 5 6</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">CONECT 3 1 4 9</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">
CONECT 4 3 5 15</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">CONECT 5 2 4 14</span><br style="color: rgb(102, 102, 102);"><span style="color: rgb(102, 102, 102);">CONECT 6 2 17 18
</span><br><span style="background-color: rgb(255, 153, 102);"></span>CONECT 17 6 10 11<br>CONECT 18 6 12 13<br><br><span style="color: rgb(51, 102, 255);">when i run x2top program i obtained</span>:<br>
<br> WARNING: masses will be determined based on residue and atom names,<br> this can deviate from the real mass of the atom type<br>Opening library file /software2/gromacs-3.3.2/exe/share/gromacs/top/aminoacids.dat
<br>Opening library file /software2/gromacs-3.3.2/exe/share/gromacs/top/atommass.dat<br>Opening library file /software2/gromacs-3.3.2/exe/share/gromacs/top/vdwradii.dat<br>Opening library file /software2/gromacs-3.3.2/exe/share/gromacs/top/dgsolv.dat
<br>#Entries in atommass.dat: 83 vdwradii.dat: 27 dgsolv.dat: 7<br>Looking whether force field files exist<br>Opening library file /software2/gromacs-3.3.2/exe/share/gromacs/top/ffoplsaa.rtp<br>Opening library file ffoplsaa.n2t
<br>WARNING: all CONECT records are ignored<br>Opening library file ffoplsaa.n2t<br>There are 21 name to type translations<br>Generating bonds from distances...<br>atom 18<br><span style="background-color: rgb(255, 255, 51);">
Can not find forcefield for atom C-2 with 2 bonds</span><br style="background-color: rgb(255, 255, 51);"><span style="background-color: rgb(255, 255, 51);">Can not find forcefield for atom C-6 with 1 bonds</span><br style="background-color: rgb(255, 255, 51);">
<span style="background-color: rgb(255, 255, 51);">Can not find forcefield for atom N-17 with 2 bonds</span><br style="background-color: rgb(255, 255, 51);"><span style="background-color: rgb(255, 255, 51);">Can not find forcefield for atom N-18 with 3 bonds
</span><br><br>-------------------------------------------------------<br>Program x2top, VERSION 3.3.2<br>Source code file: x2top.c, line: 206<br><br>Fatal error:<br>Could only find a forcefield type for 14 out of 18 atoms
<br><br><br><font style="color: rgb(51, 102, 255);" size="2">I know that i can add these atoms to the ffoplsaa.n2t file. But what i<br>don't understand is that the program says that C6 atom is attached by 1 bond, whereas
<br>in fact it's attached to 3 atoms. C2 has 3 bonds (not 2) and N17 has 3 bonds (not 2). <br>I tried to include the atoms in the ffoplsaa.n2t but i must did it in the wong connectivity.<br><br>Thanks in avance for your help and best regards,
<br><br>Patricia<br></font><br><br>