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-- 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/amberReceived on Tue Aug 25 2015 - 19:30:03 PDT