Hi,
Sorry for the delay in replying.
So just to be clear, the script:
> trajin md2.mdcrd 1000 19000 5
> strip :WAT
> strip :Na+
> trajout output.pdb pdb append
Still gives you something that looks like it exploded? By this I
assumes you mean the two strands of DNA have separated? I think this
is just an imaging issue. Try this:
trajin md2.mdcrd 1000 19000 5
strip :WAT,Na+
center :1-20 mass origin
image origin center familiar
trajout output.pdb pdb append
If you use cpptraj you can omit the 'append' keyword from the
'trajout' command since MODEL/ENDMDL keywords are added automatically
for multiple frame PDB output files.
-Dan
On Thu, Jul 5, 2012 at 1:23 PM, Gordon S Freeman <gfreeman.wisc.edu> wrote:
> Dear Amber Users,
>
> I have .mdcrd and .prmtop files that I am trying to use to generate a
> .pdb output file that x3DNA plays nicely with. The trajectory is a 20 bp
> DNA solvated in tleap by the solvateoct command. If I visualize the
> .mdcrd file, everything looks just fine. I use the following ptraj
> script to try to generate the .pdb file I need for subsequent analysis:
>
>
> The resulting .pdb file looks great for the first few thousand
> simulation frames (i.e. frames 1000 to almost 5000 from the simulation
> convert just fine) while the latter 75% of the frames produce .pdb
> structures that look like a cubic periodic box that has exploded. The
> energies and .mdcrd file look fine so an explosion is clearly not the
> explanation. Am I missing something in my ptraj input file above to
> properly deal with the non-cubic periodic box the simulation was run
> with? Does anyone have a script they have successfully used to do this
> conversion? I could easily generate the pdb using VMD and the
> correct-looking mdcrd file and then write a script to add the MODEL and
> ENDMDL flags 3DNA looks for but I'd rather get my ptraj script working
> properly.
>
> FYI, using the same script above without the lines "unwrap :1-40\ center
> :1-40 mass origin\ image origin center familiar\" also produces the same
> strange output.
>
> Thanks in advance for this and all the other help this listserve and the
> developers have provided over the years.
>
> -Gordon
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Lab Specialist
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 10 2012 - 07:30:04 PDT
