Thanks for all suggestion. Can you tell how can I get solvent accesible
surface area of selected residues .
On Tue, Oct 4, 2011 at 9:47 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Oct 4, 2011 at 1:36 AM, kirtana S <skirtana4.gmail.com> wrote:
>
> > 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.
> >
>
> In ptraj, when you issue the "trajout" command, use the "nobox" keyword to
> get rid of the box information.
>
> HTH,
> Jason
>
>
> >
> > 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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> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > 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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> > > >
> > >
> > >
> > >
> > > --
> > > 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 Thu Oct 06 2011 - 14:30:02 PDT
