Hi Dan,
Thanks for your reply.
However, this script gives me the output,
#Frame RMSD_00001
1 0.0000
Also when you say
># Align subunit A in trajectory to A in reference
> rms reference :1-277.CA
should the line be rms reference :1-138.CA ? Also I want to compute the rmsd of
subunit B wrt subunit A.
I am a little confused.
Thanks a lot in advance.
Moitrayee
> Hi,
>
> On Wed, Aug 21, 2013 at 7:25 PM, <moitrayee.mbu.iisc.ernet.in> wrote:
>> trajin ./decamer-rep-57ns.pdb.1
>> reference decamer-rep-57ns.pdb.1 :1-138.CA -> to define reference
>> rms :139-277.CA reference -> to align subunit B on A
>> rms :139-277.CA reference out rmsAB.dat nofit -> to calculate rmsd of B wrt A.
>
> For the following I'm assuming here residues 1-138 are subunit A, and
> 139-277 are subunit B.
>
> First, you're reading in your reference with a mask; the effect of
> this is to strip the reference structure so 'only' the atoms in the
> mask remain; in this case CA atoms from residues 1 to 138. Then you're
> trying to fit residues 139-277 in your input trajectory to the
> reference; but since those residues were stripped from the reference
> you should have received an error like:
>
> Error: rmsd: No reference atoms selected for parm...
>
> (If you did not receive an error message please tell me what version
> of cpptraj you are running).
>
> I think maybe what you want is to first fit on subunit A, then take
> the no-fit RMSD of subunit B, e.g.:
>
> trajin ./decamer-rep-57ns.pdb.1
> reference decamer-rep-57ns.pdb.1
> # Align subunit A in trajectory to A in reference
> rms reference :1-277.CA
> # Get the no-fit RMSD of subunit B in trajectory to B in reference;
> still fit on A
> rms nofit reference :139-277.CA out rmsAB.dat
>
> Hope this helps,
>
> -Dan
>
> --
> -------------------------
> 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
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Received on Wed Aug 21 2013 - 22:00:02 PDT
