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)
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Received on Tue Aug 25 2015 - 06:30:04 PDT
