Thank you Dan.
The “perresavg” keyword did the trick.
George
On 03 May 2015, at 00:32, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> No snapshot was attached. However, the output is exactly what it
> should be (RMSD of each individual residue vs frame). Maybe you wanted
> the 'perresavg' keyword?
>
> -Dan
>
> On Sat, May 2, 2015 at 12:37 PM, George Tzotzos <gtzotzos.me.com> wrote:
>> I’m trying to work out the average rmsd over time of each residue in a protein receptor.
>>
>> The script I’m using is the following:
>>
>> parm 4fqt_OVT_solv.prmtop [MD]
>> parm 4fqt_new.pdb [Xray]
>> trajin prod_0-20ns.nc [MD]
>> reference 4fqt_new.pdb parm 4fqt_new.pdb [4FQ]
>>
>> rmsd :10-125 reference perres perrescenter perresout PRMS.dat range 10-125 perresmask &!.H,N,CA,HA,C,O
>> run
>> xmgrace PRMS.dat
>>
>> I assume it is not correct as the output produced (see snapshot below) is not the expected one. In the x-axis instead of residue number, I get frame number.
>>
>> I’d appreciate any suggestions in correcting the above script.
>>
>> Regards
>>
>> George
>>
>>
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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
> (801) 585-6208 (Fax)
>
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Received on Sun May 03 2015 - 02:30:03 PDT
