they are chemically identical.
> Are a and b chemically identical? If not, standard rmsd does not apply.
> Bill
>
> -------- Original message --------
> From: moitrayee.mbu.iisc.ernet.in
> Date: 08/21/2013 10:01 PM (GMT-08:00)
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] RMSD calculation followed by superimposition
>
> As a continuation of my last email, I want to compute the rmsd between subunit b
> and a. So I guess I have to B on A instead of B on B.
>
>> 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
>> (801) 585-9119 (Fax)
>>
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Received on Thu Aug 22 2013 - 00:00:03 PDT
