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
> > 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
Received on Mon Oct 03 2011 - 22:30:03 PDT
