[gmx-users] NA or SOD in CHARMM36

[Jason Loo Siau Ee]

Hi all,

I'm trying to simulate a protein-ligand complex in POPC membrane using the CHARMM36 forcefield, which I got from the Mackerell site and included in /share/gromacs/top/. Now when I run grompp I get the error "Fatal error: No such moleculetype SOD" despite the fact that I have #include "charmm36.ff/ions.itp" in my topology. A quick check on the ions.itp in charmm36.ff/ shows the following:

[ moleculetype ]
; molname   nrexcl
NA      1

[ atoms ]
; id    at type     res nr  residu name at name  cg nr  charge
1   SOD     1   NA      NA   1  1

Now as I understand sodium is called SOD in CHARMM, so shouldn't all the NA be SOD instead? As this is from the Mackerell site I'm going to assume there isn't an error here, so am I about the do something silly? Is there a reason for this discrepancy (like because genion only adds NA and not SOD)? I've noticed similar issues with other ions and the water models (SOL instead of TI3P). I'm guessing I should create a local copy of the modified itp files then?

Regards,
Jason Loo








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