CHARMM36 and NAMD

From: Douglas Houston (DouglasR.Houston_at_ed.ac.uk)
Date: Tue Feb 18 2014 - 04:02:38 CST

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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The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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