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
>
>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Wed Mar 02 2011 - 01:00:03 PST
