Re: torsional restrain

From: Lara rajam (lara.4884_at_gmail.com)
Date: Thu Feb 23 2017 - 11:56:45 CST

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>
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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