AMBER Archive (2009)

Subject: Re: [AMBER] DNA simulation: Problem with RMSD

From: BERGY (nucleic81_at_gmail.com)
Date: Fri Mar 06 2009 - 00:20:00 CST

Dear Sir,
 Thank you so much for your kindly help. Now the output seems ok.

On Thu, Mar 5, 2009 at 9:34 AM, Thomas Cheatham <tec3_at_utah.edu> wrote:
>
>>  I am doing a MD simulation on a 12mer DNA, for all my RMSD ,
>> helicoidal analysis i wish to remove the terminal base pairs from the
>> analysis. How to go about.
>
> The first question is why you would want to remove the terminal base pairs
> as these are an integral part of the structure.  Plus, frequent fraying at
> the end could be indicative of instability.  Regardless, if you want to
> remove the terminii you could use the strip command
>
>> trajin traj1.mdcrd
>> trajin traj2.mdcrd
>> trajout fixed.traj
>> rms first out rms :2-11,13-23 time 0.2
>> center :1-24
>> image
>> strip :WAT
>> go
>
> OK, first problem with the above is that you are doing a box rotation with
> RMS before you are doing imaging.  This is incorrect and needs to be
> fixed.
>
> trajin traj1.mdcrd
> trajout fixed.traj
> center :1-12 mass origin
> image origin
> center :1-24 mass origin
> image origin center
> rms first out rms :2-11,13-23 time 0.2
> strip :WAT
> strip :1,12,13,24
>
> --tec3
>
>
>
>> ---------------------------------------
>> Is the format correct to calculate RMSD.  will my  fixed.traj output
>> file have the terminal base pairs removed.
>>
>> regards
>> dksenthil,
>>
>> Graduate Student
>> MBU,IISc,
>> Bangalore,
>> India
>>
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>
> \-/   Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
> -/-    Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
> /-\  Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
> \-/   University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
> -/-
> /-\      tec3_at_utah.edu         (801) 587-9652; FAX: (801) 585-9119
> \-/        BPRP295A             http://www.chpc.utah.edu/~cheatham
>
>
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