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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