Re: torsional restrain

From: Vermaas, Joshua (
Date: Thu Feb 23 2017 - 11:09:02 CST

Hi Lara,

A few things spring to mind that might be simple fixes, since the syntax looks right:

1.) I recall some parameters in NAMD being case-sensitive. In the manual, its extraBonds and extraBondsFile.
2.) Make sure the res.txt is in the right place. Should be in the same directory as the .conf/.namd file.


On 02/23/2017 09:19 AM, Lara rajam wrote:

I would like to use the torsional restraint in the simulation. I went through the manual. This is my first time of adding restraints
and added

extrabonds on

extrabondsfile res.txt

in the configuration file.

the file contents are below

dihedral 2048 2053 2060 2064 1.0 53.86

dihedral 2053 2060 2064 2050 1.0 -54.78

dihedral 2060 2064 2050 2052 1.0 58.51

dihedral 2064 2050 2052 2048 1.0 -62.73

but after minimization the run is not going with saying an error

Reason: FATAL ERROR: Setting parameter extrabonds from script failed!

Fatal error on PE 2> FATAL ERROR: Setting parameter extrabonds from script failed!

Could someone let me know what the error is where I am doing a mistake, I have also a question regarding the k spring constant value, how to specify 1.0 or 2.0


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