I am using ASCII trajectory and as this is postprocessed from original
trjectory to remove the water molecules and centered I assume this contain
the box information.
I checked for other files there is nothing wrong with my prmtop and inpcrd
files.
Is there any way I can modify my trajectory file for box information.
Thanks
kirtana
On Tue, Oct 4, 2011 at 1:09 AM, Jason Swails <jason.swails.gmail.com> wrote:
> You probably didn't create your coordinate files correctly. Try
> visualizing
> them. Do they look OK? If not, you need to make sure that you create
> compatible trajectories and topologies. Also, I think if you use igb=6 for
> vacuum you also have to make sure that you didn't save any box information
> to your md.x file if you used ASCII trajectories. If you used NetCDF
> trajectories, then you have to add ioutfm=1 to your &cntrl namelist.
>
> HTH,
> Jason
>
> On Tue, Oct 4, 2011 at 12:57 AM, kirtana S <skirtana4.gmail.com> wrote:
>
> > I want to calculate sasa for each frame of trajectory ,
> > sander -O -i sasa.in -c inpcrd -p prmtop -y md.x -o SASA.out
> >
> > &cntrl
> > imin=5,
> > gbsa=1,
> > surften=1,
> > igb=6,
> > ntb=0,
> > cut=999,
> > /
> > Simulation were using periodic boundary condition (TIP3P) and the inpcrd
> > file and prmtop file are vacuum parameter files , as well as trjactory
> file
> > (-y md.x) is also after removal of water molecules.
> > The output file gives energy (NaN) what does this imply and where am I
> > going
> > wrong .Below is a part of it .
> >
> >
> > POST-PROCESSING OF TRAJECTORY ENERGIES
> > trajectory generated by
> > ptraj
> > minimizing coord set # 1
> >
> > Maximum number of minimization cycles reached.
> >
> > FINAL RESULTS
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 1 1.5654E+00 1.9744E+01 1.0703E+02 C3 215
> > BOND = 162.0649 ANGLE = 294.1696 DIHED =
> > 311.5689
> > VDWAALS = -126.8526 EEL = -126.8534 EGB =
> > 0.0000
> > 1-4 VDW = 237.2528 1-4 EEL = -749.7848 RESTRAINT =
> > 0.0000
> > ESURF = 0.0000
> > minimization completed, ENE= 0.15653978E+01 RMS= 0.197442E+02
> > minimizing coord set # 2
> >
> > Maximum number of minimization cycles reached.
> >
> > FINAL RESULTS
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 1 NaN NaN 1.0608E+20 H1 174
> > BOND = 23725808.3931 ANGLE = 65714.0057 DIHED =
> > 4348.2709
> > VDWAALS = ************* EEL = -234.4713 EGB =
> > 0.0000
> > 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> > 0.0000
> > ESURF = 0.0000
> > minimization completed, ENE= NaN RMS= NaN
> > minimizing coord set # 3
> >
> > Maximum number of minimization cycles reached.
> >
> > FINAL RESULTS
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 1 NaN NaN 2.8942E+11 C5 11
> > BOND = 17569497.0693 ANGLE = 66359.4683 DIHED =
> > 4649.7578
> > VDWAALS = ************* EEL = -566.8816 EGB =
> > 0.0000
> > 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> > 0.0000
> > ESURF = 0.0000
> > minimization completed, ENE= NaN RMS= NaN
> > minimizing coord set # 4
> >
> > Maximum number of minimization cycles reached.
> >
> > FINAL RESULTS
> > On Mon, Oct 3, 2011 at 9:02 PM, Jason Swails <jason.swails.gmail.com>
> > wrote:
> >
> > > Why are you using gbsa=2 instead of gbsa=1? gbsa=1 doesn't have this
> > error
> > > (it just assigns it the carbon SA parameter).
> > >
> > > All the best,
> > > Jason
> > >
> > > On Mon, Oct 3, 2011 at 5:03 PM, kirtana S <skirtana4.gmail.com> wrote:
> > >
> > > > I am calculating the solvent accessible surface area od my solute .I
> > got
> > > an
> > > > error as bad atom type , following up th error I need to change in
> > > mread.f
> > > > file in sander .
> > > > Can any one help me to understand the specifications provided for the
> > > atoms
> > > > in the mdread.f file (after line 1080) ,how can I modify this for Fe.
> > > >
> > > > Thanks
> > > > Kirtana
> > > > _______________________________________________
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> > > > AMBER.ambermd.org
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> > > >
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Oct 03 2011 - 23:00:32 PDT
