Hi Sangeeta,
I am not sure but you try with generating the pdb file and then check the
structure in any other visualizer let say Pymol. i got the same problem
previously and I found that it was related to VMD.
Hirdesh
On Wed, Mar 2, 2011 at 2:11 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
> I have checked mdcrd file there is theer numbers line not six numbers line
> after
> each snapshot
> 2.121 -23.199 35.340 36.220 41.041 35.621 35.320 41.209 35.129
> 36.235
> 40.108
> 73.004 73.004 73.004
>
> In restrt file there is six numbers line at the end of file.
> I have checked in restrt file 73.004 is box size
> -0.1657884 0.4894307 -0.0631572 0.2706823 0.5604288 -0.8288725
> -0.6596030 0.8937120 0.1677584
> 73.0044927 73.0044927 73.0044927 109.4712190 109.4712190 109.4712190
>
> when I removed box size using command
> $ awk 'NF != 3' mdcrd > boxless_mdcrd
>
> from mdcrd file and load it to VMD with new prmtop having protein-DNA + 10
> water
> molecule
> again there is same problem i.g. some long bonds formation.
>
>
>
>
> > 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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> >
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>
>
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
>
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Received on Wed Mar 02 2011 - 01:30:04 PST
