[gmx-users] X2top usage

[Ben Tam]

Dear gromacs user.


I am using gmx x2top to write a rough connectivity map for the crystal structure that I am using. In the conf.gro file, there are many ions with no bond to any other molecules. How do I specify that on .n2t file? Because when I do specify it with:

Mg   Mg          0.000  24.3050 0


It is still giving me the error of :


Can not find forcefield for atom Mg-1245 with 0 bonds
Can not find forcefield for atom Mg-1254 with 0 bonds
Can not find forcefield for atom Mg-1263 with 0 bonds
Can not find forcefield for atom Mg-1272 with 0 bonds
Can not find forcefield for atom Mg-1281 with 0 bonds
Can not find forcefield for atom Mg-1290 with 0 bonds
Can not find forcefield for atom Mg-1299 with 0 bonds
Can not find forcefield for atom Mg-1308 with 0 bonds
Can not find forcefield for atom Mg-1317 with 0 bonds
Can not find forcefield for atom Mg-1326 with 0 bonds
Can not find forcefield for atom Mg-1335 with 0 bonds
Can not find forcefield for atom Mg-1344 with 0 bonds
Can not find forcefield for atom Mg-1353 with 0 bonds
Can not find forcefield for atom Mg-1362 with 0 bonds
Can not find forcefield for atom Mg-1371 with 0 bonds
Can not find forcefield for atom Mg-1380 with 0 bonds
Can not find forcefield for atom Mg-1389 with 0 bonds
Can not find forcefield for atom Mg-1398 with 0 bonds
Can not find forcefield for atom Mg-1407 with 0 bonds
Can not find forcefield for atom Mg-1416 with 0 bonds
Can not find forcefield for atom Mg-1425 with 0 bonds
Can not find forcefield for atom Mg-1434 with 0 bonds
Can not find forcefield for atom Mg-1435 with 0 bonds

Thank you very much,

Best regards,

Ben