[gmx-users] NA or SOD in CHARMM36

Jason Loo Siau Ee JasonSiauEe.Loo at taylors.edu.my
Thu Apr 21 11:42:18 CEST 2016

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?

Jason Loo

Confidentiality Disclaimer: This e-mail and any attachments are confidential and intended solely for the intended addressee and may also be privileged or exempt from disclosure under applicable law. If you are not the intended addressee, or have received this e-mail in error, please notify the sender immediately, delete it from your system and do not copy, disclose, distribute or otherwise act in reliance upon any part of this e-mail or its attachments. Taylor's Education Group does not accept responsibility for any loss arising from unauthorized access to, or interference with, any internet communications by any third party in reliance to this email, or from the transmission of any viruses. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of Taylor's Education Group. Replies to this e-mail may be monitored by Taylor's Education Group for operational or business reasons.

More information about the gromacs.org_gmx-users mailing list