Hi,
On Fri, Mar 20, 2015 at 4:03 AM, jacob wick <jacobwick.la.gmail.com> wrote:
> rms first out rna_test.rms .!P,O3',O5',C3',C4',C5' time 0.50 nofit
That is not a valid atom mask. If you meant to say "not atoms P, O3',
O5'" etc (i.e. the opposite of your first mask) just put the "not"
character (!) in front, e.g.
!(.P,O3',O5',C3',C4',C5')
See section 28.2.3 in the Amber 14 manual for more information on atom
mask syntax.
Hope this helps,
-Dan
>
>
> Thanks.
> Jac
>
> On Tue, Mar 17, 2015 at 5:22 PM, David A Case <case.biomaps.rutgers.edu>
> wrote:
>
>> On Mon, Mar 16, 2015, jacob wick wrote:
>> >
>> > rms first out rna_run.rms .P,O3',O5',C3',C4',C5' time 0.50
>> >
>> > Is this script helping in comparing backbone of reference with the
>> backbone
>> > of frames (without taking residues deviations in account) or it is
>> > superimposing the reference backbone with the backbones of frame and
>> giving
>> > the deviations with respect to the residues?
>>
>> The former. A command like this superimposes frames on the backbone atom,
>> and reports the RMS value computed over the same set of atoms.
>>
>> If you want to fit on one set of atoms, but calculate the deviations for a
>> second set of atoms, you need two rms commands. The first is like that
>> above,
>> which will do the superposition. The second one would have a different
>> atom
>> mask, and the keyword "nofit", so that no additional fitting would be
>> performed.
>>
>> Play with this a bit on some very simple system to see what is going on.
>>
>> ....dac
>>
>>
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>>
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--
-------------------------
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
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Received on Sat Mar 21 2015 - 09:00:03 PDT
