[gmx-users] Crystallographic Ions
Parker de Waal
Parker.deWaal at vai.org
Tue Sep 22 21:38:05 CEST 2015
I'm working with a protein which contains 2 crystallographic sodium ions and am experiencing trouble making the .gro file using pdb2gro using the Charmm36.ff parameters.
The two ions can be seen here:
ATOM 29009 NA NA 1 -18.056 -14.113 -24.865 1.00 0.00
ATOM 29010 NA NA 2 27.831 26.294 -32.202 1.00 0.00
Whenever I run pdb2gro the program complains that NA is not a valid atom type, however whenever I manually change the ions to atom and res type to SOD the resulting .top file does not count the molecules correctly.
[ molecules ]
; Compound #mols
Other 1 (should be NA+ and 2?)
If anyone could help fix this problem I would greatly appreciate it.
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