But the command is still not working.
I am trying:
trajin ../nowat12ns.mdcrd
autoimage
rms first out activesite.dat :377<:5.0
and I am getting following error:
selectDistd(): No coordinate info for distance operator.
Error: selectDistd failed.
Error: AmberParm::SetupAtomMask: charmask is NULL.
Warning: Setup failed for [rms first out activesite.dat :377<:5.0]: Skipping
On Tue, Feb 5, 2013 at 8:07 PM, HM <scienceamber.gmail.com> wrote:
> Thanks Daniel for your all time support. :-)
>
> HM
>
>
> On Tue, Feb 5, 2013 at 6:20 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Oops. It has been pointed out to me that I made a bit of a mistake in
>> the script I gave; you shouldn't give both 'first' and 'reference' to
>> an RMS command ('first' will always take priority). This:
>>
>> reference initial
>> trajin traj
>> rms reference out rmsd.dat :LIG<:5.0
>>
>> is indeed what I meant. That's what happens when I write commands
>> before finishing my coffee. However, note that you could also do:
>>
>> reference initial
>> trajin traj
>> rms first out rmsd.dat :LIG<:5.0
>>
>> This will use 'initial' for the distance-based mask parsing, but the
>> first frame for RMSD.
>>
>> -Dan
>>
>> On Tue, Feb 5, 2013 at 8:37 AM, Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>> > Hi,
>> >
>> > If you give ptraj or cpptraj a reference structure you can do
>> > distance-based mask parsing based on that reference structure, e.g.:
>> >
>> > reference initial
>> > trajin traj
>> > rms first reference out rmsd.dat :LIG<:5.0
>> >
>> > Will get the RMSD of all residues within 5.0 angstroms of residue LIG
>> > based on the structure in 'initial'. See the manual for more details
>> > on distance-based mask parsing.
>> >
>> > -Dan
>> >
>> > On Tue, Feb 5, 2013 at 6:40 AM, HM <scienceamber.gmail.com> wrote:
>> >> Hi All,
>> >> I am interested in calculating the rmsd of the active site region i.e.
>> 5 A
>> >> around bound ligand. But as the number of those residues changes from
>> >> trajectories to trajectories, I am not sure how to tell ptraj or
>> cpptraj to
>> >> calculate rmsd for active site region.
>> >> _______________________________________________
>> >> 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 201
>> > Salt Lake City, UT 84112-5820
>> > http://home.chpc.utah.edu/~cheatham/
>> > (801) 587-9652
>> > (801) 585-9119 (Fax)
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-9119 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Tue Feb 05 2013 - 12:00:03 PST
