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
> > > > > _______________________________________________
> > > > > 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
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> > > > 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
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Oct 04 2011 - 07:00:04 PDT
