Re: SOD topology with CHARMM36

From: Kenno Vanommeslaeghe (
Date: Tue Nov 11 2014 - 12:27:08 CST

The rationale behind this is that people simulating e.g. RNA folding need
waters and ions, but not protein parameters. In other words, CHARMM36 has
been made modular. Unfortunately, we realized too late that while this
modularity works with CHARMM, it doesn't work with NAMD. The reason for
this is that toppar_water_ions.str contains NBFIXes between sodium and all
carboxylates in the different parts of the force field, so *all* parts of
the force field that contain carboxylate groups need to be read into NAMD
prior to toppar_water_ions_namd.str , else it crashes. In this context, it
would probably be nice if the error emitted when encountering an NBFIX
with an undefined atom type would be made nonfatal.

A little bit more end-user-oriented info here:

On 11/11/2014 12:08 PM, Josh Vermaas wrote:
> toppar_water_ions.str has it. You'll need to split the file up into
> topology and parameter components to keep VMD/psfgen's parsers happy, but
> thats where the waters and ions wandered off to.
> -Josh
> On 11/11/2014 11:02 AM, Francesco Pietra wrote:
>> Hello:
>> I was unable to find the topology
>> in charmm36. I added to charmm36 that from all27 in order to satisfy vmd
>> -dispdev ...
>> thanks for advice
>> francesco pietra

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:23:00 CST