From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Jul 18 2011 - 16:01:26 CDT
It looks to me like you are trying to start dynamics from your original
unminimized complex_ionized.pdb coordinates.
Since from your previous email you have binaryOutput no you need to
replace ../common/complex_ionized.pdb with ../common/complex_eq.coor.
Otherwise you would use binCoordinates as you have commented out.
-Jim
On Wed, 29 Jun 2011, bharat gupta wrote:
>
> This is my equilibration configuration file:-
>
> structure ../common/complex_ionized.psf
> coordinates ../common/complex_ionized.pdb # not taken into
> account
> #binCoordinates ../common/complex_eq.coor # this one instead
> extendedSystem ../common/complex_eq.xsc
> outputname equilibrated
> cutoff 12.0
> exclude scaled1-4
> 1-4scaling 1.0
> switching on
> switchdist 8.0
> DCDFreq 1000
> restartFreq 1000
> parameters ../common/par_all27_prot_na.prm
> paraTypeCharmm on
>
> berendsenPressure on
> berendsenPressureTarget 1.01325 # atmospheric pressure
> berendsenPressureCompressibility 4.57e-5 # liquid water
> berendsenPressureRelaxationTime 100.0
> berendsenPressureFreq 10
>
> temperature 0.5 # starting at 0.5 K
> reassignFreq 100
> reassignIncr 0.5
> reassignHold 300 # target T: 300 K
> numsteps 100000 # 100 ps, constant T the last 40 ps
>
>
> Can anybody tell be how to rectify the errors for those atoms.
>
>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010_at_yahoo.com
>
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