On Sun, Feb 10, 2013 at 8:15 PM, Joe Passman <joepassman.comcast.net> wrote:
>
>
> Hello all,
>
>
> I am setting up a 10 solvated systems. I am using a tleap to solvate the
> 10 peptides. As the proteins have different radii of gyration, each system
> has a different number of atoms.
>
>
> I would like to use cpptraj to trim down the number of water residues
> while maintain a periodic box. I am calling cpptraj twice for the following
> reasons:
>
>
> (1) Generate a .crd file with 315963 atoms
>
>
> Input file called with 'cpptraj -p parm_wb_lambdaN_100.prmtop -i
> TrajIn1.in' :
>
>
>
> trajin wb_lambdaN_100.crd
> strip :WAT&!(:50000-155000)
> trajout wb_strip_lambdaN_100.crd nobox
>
>
>
>
> (2) Generate the corresponding .prmtop file
>
>
> Input file called with 'cpptraj -p parm_wb_lambdaN_100.prmtop -i
> TrajIn2.in'
>
>
>
> trajin wb_lambdaN_100.crd
> parmstrip :WAT&!(:50000-155000)
> parmwrite out wb_strip_lambdaN_100.prmtop
>
>
> When I run these scripts and visualize in VMD, I am creating a solvated
> system that is not boxlike at all. Is there a easy way to do this?
>
>
> I read about using the 'closest' command to keep a certain number of
> waters around a solute. However, I do not know of a way to generate a
> .prmtop file. It's been suggested on the forum (
> http://archive.ambermd.org/201008/0537.html ) to create a pdb with ptraj,
> then move on to leap to generate a .prmtop via 'saveamberparm'. However, my
> system is over the number of atoms supported (99,999) within the .pdb
> format.
>
Why doesn't parmstrip work?
ParmEd also strips topology files, but it's the same concept as what
cpptraj is doing...
I suggest trying to make the original boxes in tleap so that the number of
waters is as close to possible to the target number (while still going
'over', since there's no inverse 'strip' command).
If you remove a large number of waters, then you will need to be much more
careful about how you remove the extra waters and adjust the box size. If
you only remove a small number, then the solvent density should equilibrate
pretty quickly when you run MD at NPT.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Feb 10 2013 - 19:00:02 PST
