On Sat, Nov 15, 2008 at 10:33 AM, Siddharth Rastogi wrote:
> I have removed water from mdcrd file using ptraj.
Did you build a new prmtop file without the waters?
> $AMBERHOME/exe/sander -O SASA.in -o SASA.out -p TY.top -c TY.crd -x
> TY.mdcrd
This input line is missing a '-i' before SASA.in (although it may just
have been a typo)
> if in the above line if I use -x TY.mdcrd :The error is : Unit 24 Error on
> OPEN: inptraj
That's because you did not give it an inptraj file...
> if I use -y TY.mdcrd : There is no error but under results I have the
> following :Post processing of trajectory energies and Trajectory file ended
That may be because of the prmtop file. As I mentioned earlier (and so
did Carlos) when you remove the waters did you also create a new
prmtop file, without the waters? Also, the inpcrd file should be
without the waters (in your case, this is the TY.crd file). Assuming
you have all the files correctly (no waters), the syntax:
$AMBERHOME/exe/sander -O -p prmtop -i mdin -c inpcrd -o mdout -y inptraj
should work fine.
HTH,
--
Gustavo Seabra
Postdoctoral Associate
Quantum Theory Project - University of Florida
Gainesville - Florida - USA
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Received on Fri Dec 05 2008 - 14:56:58 PST
