Re: [AMBER] closest command in cpptraj

From: Joseph Baker <bakerj.tcnj.edu>
Date: Mon, 24 Aug 2015 10:17:22 -0400

Thanks, Dan! I'll give this a shot and let you know if it works out for me.
I won't be using the topology for anything else. This is purely a data
reduction endeavor since I only need a solvation shell or two of my mixed
solvent around the solute for analysis, and want to get rid of all of the
excess stuff to save hard drive space.

Joe

--
Joseph Baker, PhD
Assistant Professor
Department of Chemistry
C101 Science Complex
The College of New Jersey
Ewing, NJ 08628
Phone: (609) 771-3173
Web: http://bakerj.pages.tcnj.edu/
<https://sites.google.com/site/bakercompchemlab/>
On Fri, Aug 21, 2015 at 5:46 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> This is certainly an interesting problem! Unfortunately it's not one
> that the 'closest' command can currently handle (need to pop another
> thing on the to-do list).
>
> However, you might be able to get what you want using two 'closest'
> commands and combinecrd. Something like this:
>
> # Load topology, mark A as solvent, get closest 10
> parm myparm.parm7
> solvent :A
> loadcrd mytraj.nc ClosestA
> crdaction ClosestA closest 10 <mask>
>
> # Reload topology, mark B as solvent, get closest 15
> clear parm
> parm myparm.parm7
> solvent :B
> loadcrd mytraj.nc ClosestB
> crdaction ClosestB closest 15 <mask>
> strip <mask>
>
> # Combine COORDS sets, write topology and trajectory
> combinecrd ClosestA ClosestB parmname CombinedParm crdname Combined
> # parmindex 1 should be the combined parm
> parmwrite out Combined.parm7 1
> crdout Combined Combined.nc
>
> In this case you should (hopefully) end up with Combined.parm7 and
> Combined.nc which contains your solute, 10 of A, and 15 of B. Note
> that I have not tested this input so I'll be surprised if it works off
> the bat, but in theory it should work. Try it on a small subset of
> your trajectory (say 10 frames or so) first.
>
> Also note DO NOT use the topology generated this way for anything but
> analysis/visualization since 'combinecrd' does not deal with
> parameters.
>
> Hope this helps,
>
> -Dan
>
>
> On Fri, Aug 21, 2015 at 1:31 PM, Joseph Baker <bakerj.tcnj.edu> wrote:
> > Hi all,
> >
> > I have a system with a solute and a two-component solvent (let's say the
> > solvent residues are A and B). I'd like to produce a trajectory/topology
> > file pair with just the solute and the N closest A molecules and M
> closest
> > B molecules to the solute. It doesn't seem that using the solvent and
> > closest commands in cpptraj I am able to get both of these simultaneously
> > (note that A and B have different numbers of atoms). Is there some way to
> > do this within cpptraj that I am missing?
> >
> > Thanks,
> > Joe
> >
> > --
> > Joseph Baker, PhD
> > Assistant Professor
> > Department of Chemistry
> > C101 Science Complex
> > The College of New Jersey
> > Ewing, NJ 08628
> > Phone: (609) 771-3173
> > Web: http://bakerj.pages.tcnj.edu/
> > <https://sites.google.com/site/bakercompchemlab/>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Mon Aug 24 2015 - 07:30:04 PDT