Hi Dan,
I'm trying to go back to the loadcrd approach to streamline this a bit, but
when I include the solvent :A and crdaction closestA closest 10 :1-4 lines,
I get an error from cpptraj that
Warning: Parm test.parm7 does not contain solvent.
So it seems like the solvent :A command isn't compatible with a trajectory
that is loaded using loadcrd? Script I am currently using is pasted below.
parm ../../test.parm7
loadcrd test.nc closestA
solvent :A
crdaction closestA strip :B outprefix noB
crdaction closestA closest 10 :1-4
crdaction closestA autoimage
crdout closestA noB.nc
run
On Wed, Aug 26, 2015 at 10:49 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Ok, I see the issue now - it's a small error on my part in the initial
> input I gave you. By default, when you enter an Action in cpptraj it
> goes into the Action list (or Action queue). Actions in the Action
> list operate on frames from input trajectories. Coordinates data sets
> are separate from this, which is why the 'crdaction' command exists.
> These concepts are explained a bit more in the Amber 15 manual
> sections 29.1.3/29.1.4 and 29.4.
>
> If you want to strip a coordinates dataset you would use crdaction
> with strip, e.g.
>
> loadcrd test.nc 1 10 ClosestA
> crdaction ClosestA strip :B
>
> will strip residues matching ':B' from the ClosestA coordinates set.
> Does that make more sense now? Let me know if you have more questions.
>
> -Dan
>
> On Tue, Aug 25, 2015 at 8:21 PM, Joseph Baker <bakerj.tcnj.edu> wrote:
> > Hi Dan,
> >
> > Sorry, no warnings or errors. Was just running up against the strip
> > commands not seeming to influence things that had been read in using
> > loadcrd. For example, the strip :1-4 didn't get rid of those solute
> > residues. Also, if I tried to add a strip command after loadcrd like
> below
> > (in just a simple script)
> >
> > parm test.parm7
> > solvent :A
> > loadcrd test.nc 1 10 ClosestA
> > strip :B
> > crdaction ClosestA closest 10 :1-4
> > crdout ClosestA Combined.pdb
> >
> > B does not get stripped from the resulting trajectory written by crdout.
> So
> > basically it was finding the closest A and B, but was not getting rid of
> > all of the other A's and B's (which got kept as part of the solute).
> >
> > The cpptraj version is 15.00
> >
> > 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 Tue, Aug 25, 2015 at 9:23 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> Hi,
> >>
> >> I'm glad you got something that works for you. Out of curiosity, what
> >> problems were you having with 'crdaction' (specific error/warning
> >> messages etc)? Also, what version of cpptraj are you using?
> >>
> >> -Dan
> >>
> >>
> >> On Mon, Aug 24, 2015 at 1:34 PM, Joseph Baker <bakerj.tcnj.edu> wrote:
> >> > I was having trouble getting the crdaction commands to work, but I
> took
> >> > your workflow and chunked up the procedure into various parm and
> trajin
> >> > lines, and the script below seems to very nearly work like a charm.
> The
> >> > last remaining problem is that it seems to produce two copies of the
> >> solute
> >> > (resid 1-4 in this case), so that strip command down below the second
> >> > loadcrd doesn't seem to be doing anything. Any idea there?
> >> >
> >> > Thanks again,
> >> > Joe
> >> >
> >> >
> >> > #get first solvent, strip second solvent so it doesn't get considered
> as
> >> > part of the solute later during closest command
> >> > parm test.parm7
> >> > trajin test.nc 1 10
> >> > strip :B outprefix noB
> >> > autoimage
> >> > trajout noB.nc
> >> > run
> >> >
> >> > #clear parm and traj
> >> > clear parm
> >> > clear trajin
> >> >
> >> > #get second solvent, strip first solvent so it doesn't get considered
> as
> >> > part of the solute later during closest command
> >> > parm test.parm7
> >> > trajin test.nc 1 10
> >> > strip :A outprefix noA
> >> > autoimage
> >> > trajout noA.nc
> >> > run
> >> >
> >> > #clear parm and traj
> >> > clear parm
> >> > clear trajin
> >> >
> >> > #read trajectory with solvent A, find closest
> >> > parm noB.test.parm7
> >> > trajin noB.nc
> >> > solvent :A
> >> > closest 30 :1-4 noimage outprefix noB-closest
> >> > trajout noB-closest.nc
> >> > run
> >> >
> >> > #clear parm and traj
> >> > clear parm
> >> > clear trajin
> >> >
> >> > #read trajectory with solvent B, find closest
> >> > parm noA.test.parm7
> >> > trajin noA.nc
> >> > solvent :B
> >> > closest 30 :1-4 noimage outprefix noA-closest
> >> > trajout noA-closest.nc
> >> > run
> >> >
> >> > #clear parm and traj
> >> > clear parm
> >> > clear trajin
> >> >
> >> > #read in both of the trajectories with just closest solvent molecules
> >> > parm noB-closest.noB.test.parm7
> >> > loadcrd noB-closest.nc noB
> >> >
> >> > clear parm
> >> >
> >> > parm noA-closest.noA.test.parm7
> >> > loadcrd noA-closest.nc noA
> >> > strip :1-4
> >> >
> >> > #combine together into one file
> >> > combinecrd noB noA parmname CombinedParm crdname Combined
> >> > parmwrite out Combined.parm7 1
> >> > crdout Combined Combined.nc
> >> >
> >> >
> >> > --
> >> > 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 Mon, Aug 24, 2015 at 10:17 AM, Joseph Baker <bakerj.tcnj.edu>
> wrote:
> >> >
> >> >> 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)
> >> >>>
> >> >>> _______________________________________________
> >> >>> 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
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> 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)
> >>
> >> _______________________________________________
> >> 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
>
>
>
> --
> -------------------------
> 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)
>
> _______________________________________________
> 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
Received on Mon Sep 07 2015 - 11:30:03 PDT
