Re: Problem with parameter file in Pair Interaction Calculation

From: Boyang Wang (pkuwangboyang_at_gmail.com)
Date: Mon Jan 09 2012 - 08:27:02 CST

Hi Mohammad,

you can try to comment or delete the line of error, or restart your
computer, and then your file might work. You can also use a new file
instead.

Good luck,

Boyang

On Mon, Jan 9, 2012 at 7:47 PM, M Mahjour <m.ali_mahjour_at_yahoo.com> wrote:

>
> Dear all,
>
> I would appreciate that if inform me to prepare a right strategy on my
> problem.
> I need to solve this error:
>
> FATAL ERROR: UNKNOWN PARAMETER IN XPLOR PARAMETER FILE
> par_all27_prot_lipid.inp
> LINE=c
>
> By the way, I've used this parameter file in my simulation package and I
> didn't have any problem with that !
>
> For more clarity I brought my Pair Interaction configuration file as below:
>
>
> # initial config
> coordinates AAA11_p.pdb
> temperature 0
>
> # output params
> outputname AAA11_p-analyze
> binaryoutput no
>
> # integrator params
> timestep 1.0
>
> # force field params
> structure AAA11_p.psf
> parameters par_all27_prot_lipid.inp
> exclude scaled1-4
> 1-4scaling 1.0
> switching on
> switchdist 8.0
> cutoff 12.0
> pairlistdist 13.5
> stepspercycle 20
>
> # Atoms in group 1 have a 1 in the B column; group 2 has a 2.
> pairInteraction on
> pairInteractionFile AAA11_p_analyze.pdb
> pairInteractionCol B
> pairInteractionGroup1 1
> pairInteractionGroup2 2
>
> # First frame saved was frame 1000.
> set ts 1000
>
> coorfile open dcd AAA11_p.dcd
>
> # Read all frames until nonzero is returned.
> while { ![coorfile read] } {
> # Set firstTimestep so our energy output has the correct TS.
> firstTimestep $ts
> # Compute energies and forces, but don't try to move the atoms.
> run 0
> incr ts 1000
> }
> coorfile close
>
>
> Previously, thank you for your consideration.
>
> Sincerely yours,
> Mohammad
>

-- 
Boyang Wang, Ph.D.

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