Look at your mdcrd file and see if you can identify the box lines.
Likely they all have six numbers for coordinates and angles, and
angles in them that are the same. Assuming these are the only
lines with six numbers, you could strip by
$ awk 'NF != 6' mdcrd > boxless_mdcrd
If e.g. the line before each box also happens to have 6 numbers,
you will have to be more creative to avoid deleting those lines.
E.g. if an angle is given as 90.000,
$ awk 'NF != 6 && $4 != "90.000"' mdcrd > boxless_mdcrd
> But sorry how to strip box to make compatible with new topology?
>
> >> Convert this to pdb file, modify pdb retain only 10 water and then use it to
> >> generate new topology file in tleap.
> >
> > Presumably there is no box.
> >
> >> When I use this topology file to visualize above processed trajectry file
> >> structure was not proper there is some long bonds.
> >
> > Maybe there's a box in mdcrd? If so, you would need to strip
> > it to be compatible with the the new prmtop.
> >
> > Bill
> >
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> >
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
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Received on Tue Mar 01 2011 - 12:30:04 PST
