[gmx-users] OPLS force field issue....

[sidath1]

Justin,

As i understood from reading and tutorial what i should do is, lets say i
generated a topology file named as
topol.top, so i need to add #include "oplsaa.ff/ions.itp" so it accounts for
Na+.

my question is..

1.how can i get rid of sodium? just removing the corresponding lines from
the .pdb text?
2. i tried with uncharged system for simplicity with less number of atoms..(
here i replaced the COONa functional group with a CH3 group)

but still g_x2top -f test.pdb -o np1.top -name np1 -ff oplsaa -pbc

am getting this parameters missing..

Can not find forcefield for atom C-147 with 1 bonds
Can not find forcefield for atom C-148 with 1 bonds
Can not find forcefield for atom C-873 with 1 bonds
Can not find forcefield for atom C-874 with 1 bonds
Can not find forcefield for atom C-939 with 1 bonds
Can not find forcefield for atom C-940 with 1 bonds
Can not find forcefield for atom C-1137 with 1 bonds
Can not find forcefield for atom C-1138 with 1 bonds
Can not find forcefield for atom C-1269 with 1 bonds
Can not find forcefield for atom C-1270 with 1 bonds

for that do i need to modify the atomname2type.n2t  the way i did earlier?or
am i doing this wrong?

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