Thanks for reply
Actualy what is my problem that I have to study water mediated H-bond betwen
protein - DNA complex during MD simulation
so what I did processed mdcrd file to retain prodtein-DNA complex and 10 water
molecule
close to 115th residue using closest command.
I also prepare new prmtop for protein-DNA complex and 10 water molecules
by taking a snapshort form mdcrd file convert it to PDB and modify the PDB so
taht it contains
only protein-DNA and 10 water molecules.
When I load processed mdcrd with new prmtop its not showing structure properly
there is some long bonds.
> 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
>> >> >
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >
>> >
>> >
>> >> Sangita Kachhap
>> >> JRF
>> >> BIC,IMTECH
>> >> CHANDIGARH
>> >
>> >
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 02 2011 - 02:00:02 PST
