Dear users,<br><br>pdb2gmx -f xxx.pdb<br>water:spc<br>forcefield:43a1<br>editconf -f conf.gro -bt cubic -d 1.0 -o box.gro<br>genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro<br>grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr<br>
<b>Fatal error:</b><br>number of coordinates in coordinate file (solvated.gro, 106523) does not match topology (topol.top, 106553)<br>I look at gmx-user search. But I dont be able to solved the problem. Then I look at conf.gro and box.gro. I recognised the there is not the TRS ligand in the box.gro file. What reason?<br>
<br>Thanks in advance<br><br><u><b>conf.gro:</b></u><br>MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE<br> 5354<br> 2GLN N 1 1.458 -1.158 0.739<br> 2GLN H1 2 1.520 -1.083 0.763<br>...<br> 485HOH HW1 5333 0.221 -3.864 -2.291<br>
485HOH HW2 5334 0.303 -3.946 -2.407<br> 1EDO OAB 1 0.625 -3.071 -0.171<br> 1EDO HAA 2 0.698 -3.048 -0.107<br> 1EDO CAA 3 0.596 -3.211 -0.163<br> 1EDO CAC 4 0.486 -3.247 -0.261<br>
1EDO OAD 5 0.365 -3.179 -0.224<br> 1EDO HAB 6 0.292 -3.203 -0.288<br> 1TRS O1 1 1.825 -3.900 0.047<br> 1TRS HAA 2 1.853 -3.860 -0.040<br> 1TRS C1 3 1.712 -3.977 0.028<br>
1TRS C 4 1.659 -4.044 0.150<br> 1TRS C3 5 1.576 -3.946 0.226<br> 1TRS O3 6 1.634 -3.824 0.256<br> 1TRS HAC 7 1.569 -3.768 0.307<br> 1TRS N 8 1.582 -4.159 0.113<br>
1TRS HAE 9 1.547 -4.204 0.195<br> 1TRS HAF 10 1.505 -4.131 0.056<br> 1TRS HAD 11 1.639 -4.223 0.062<br> 1TRS C2 12 1.776 -4.085 0.233<br> 1TRS O2 13 1.887 -4.122 0.160<br>
1TRS HAB 14 1.961 -4.148 0.222<br> 8.13100 7.04165 13.54850 0.00000 0.00000 -4.06550 0.00000 0.00000 0.00000<br><br><br><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>