Re: torsional restrain

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Feb 23 2017 - 12:02:18 CST

Wait, this is after a run command? That is the problem. :) There are certain things you can adjust after the first run or minimization command is issued, and adding extrabonds isn't one of them. Push the extrabonds specifications above your first run/minimize statement.

-Josh

On 02/23/2017 10:56 AM, Lara rajam wrote:
Dear Joshua !
Thank you , for the reply ..
I have changed the file name but, still I get the error message. I moved the restrain file next to minimization steps
and the res.txt is in the same path
the error is as below

The last position output (seq=-1) takes 0.004 seconds, 23.830 MB of memory in use

WRITING VELOCITIES TO OUTPUT FILE AT STEP 4000

The last velocity output (seq=-1) takes 0.001 seconds, 23.581 MB of memory in use

TCL: Setting parameter extraBonds to on

FATAL ERROR: Setting parameter extraBonds from script failed!

FATAL ERROR: Setting parameter extraBonds from script failed!

Is there any suggestions to fix this thank you

On Thu, Feb 23, 2017 at 12:09 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>> wrote:
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.

-Josh

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

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

thanks

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