Re: CHARMM36 and NAMD

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Tue Feb 18 2014 - 20:23:37 CST

We are providing a separate version of toppar_water_ions.str for NAMD
users. The offending lines (which are not present in said
toppar_water_ions_namd.str ) give users of the CHARMM program the
flexibility to read any combination of parameter files without having to
worry about the NBFIXes. In NAMD, the easiest way to make sure that all
the necessary NBFIXes are always in effect is to read *all* the CHARMM36
parameter files into NAMD prior to reading toppar_water_ions_namd.str :
http://mackerell.umaryland.edu/~kenno/cgenff/program.html#namd

On 02/18/2014 05:02 AM, Douglas Houston wrote:
> Hi all,
>
> I have a question re. the new CHARMM36 force field. To get the
> toppar_water_ions.str file (downloaded from
> http://mackerell.umaryland.edu/CHARMM_ff_params.html) to work with NAMD I
> had to comment out several lines to avoid fatal error messages.
>
> For example:
>
> FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE
> toppar/toppar_water_ions.str
> LINE=*set nat ?NATC*
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE
> toppar/toppar_water_ions.str
> LINE=*set nat ?NATC*
>
> Fatal error on PE 0> FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER
> FILE toppar/toppar_water_ions.str
> LINE=*set nat ?NATC*
>
>
> Is this due to a mismatch between the program these files were apparently
> designed for (CHARMM) and NAMD, and does commenting out these lines do any
> harm? For example, the file says "IMPORTANT NOTE: this file contains
> NBFixes between carboxylates and sodium which will only apply if the main
> files containing carboxylate atom types have been read in first!"
>
> By commmenting out all of the lines NAMD chokes on am I deactivating these
> NBfixes?
>
> _____________________________________________________
> Dr. Douglas R. Houston
> Lecturer
> Room 3.23
> Institute of Structural and Molecular Biology
> Michael Swann Building
> King's Buildings
> University of Edinburgh
> Edinburgh, EH9 3JR, UK
> Tel. 0131 650 7358
>

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