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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 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 - 13:00:03 PDT