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
>
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Received on Mon Oct 03 2011 - 22:00:03 PDT
