Re: Protein-ligand simulation

From: Kenno Vanommeslaeghe (
Date: Fri Jun 28 2013 - 12:22:12 CDT

On 06/28/2013 05:21 AM, James Starlight wrote:
> 2013/6/28 Irene Newhouse < <>>
> if you have an
> independent set of ligand parameters, there is no way I know of to
> use 2 separate files. You'll have to edit the ligand parameters into
> the NAMD parameter file you intend to use for the protein.

For the record, this might have been true at some point in the past, but
if so, it stopped being true several years ago. In the more recent
versions of NAMD, one can read more than one parameter file, as in this
In fact, we strongly discourage editing the main parameter files as found
in the CHARMM distribution for purposes other than modifying the force
field. We've had several cases of users complaining about incorrect
behavior because
- they unwittingly were using a modified version of the parameter files
that was staged to a common area by someone else in their lab
- they tried to merge the parameter files themselves but failed to do it
correctly (yes I know it's very easy but this really happened - several
times in fact)



This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:22 CST