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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 Mon, Aug 24, 2015 at 3:34 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/amberReceived on Mon Aug 24 2015 - 14:30:04 PDT