[gmx-users] problem with Na+ ions....

[Rahul Karyappa]

Dear all,

    I have structure with defined Na ions in it. I have
a .pdb file of that structure and I want to convert it to .gro and .top
files. When I tried it on PRODRG website it gave me error that Na+ is
not supported. Then I defined all the atoms in .rtp file also Na. But
it's not working. What can I do for this? I have included "ions.itp"
file in the .top file. Do I need to delete the Na+ entry in the .top
file. I can't delete them from .gro file because their coordinates are
specified. What Should I do?

Thanking you in advance.


Rahul Karyappa

NCL, India




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