Thank you once again
perresavg produced what I expected. I then tried to filter the residues with the highest RMSD values by adding a line to the script as shown here:
rmsd A :11-125 ref [struct0] perres perresavg PRMS.avg.dat range 11-125 perrescenter perresmask &!.H,N,CA,HA,C,O
filter A min 2.5 max 8.0 out FilteredRes.dat
The output is not what I would expect see an example of part of the output below
475 1
476 0
477 1
478 1
479 1
Obviously the l.h.s column represents frame number rather than residue number.
I’d appreciate any suggestions regarding the correct syntax of the filter line.
Best wishes
George
> On 18 Aug 2015, at 17:53, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> I don't think there's anything wrong with your script - from the Amber
> 15 manual:
>
> ...
> perresout <perresfile> Write per-residue RMSD to <perresfile>.
> perresavg <avgfile> Write average per-residue RMSDs to <avgfile>.
> ...
>
> So it sounds like what you want might be 'perresavg'.
>
> -Dan
>
> On Tue, Aug 18, 2015 at 8:47 AM, George Tzotzos <gtzotzos.me.com> wrote:
>> Following the AmberTools15 manual (p. 552), I’m using the following input scrip to do a per-residue RMSD calculation:
>>
>> parm complex_solv.prmtop
>> trajin prod_0-100ns.nc 1 10000 10
>> reference complex_solv.inpcrd [struct0]
>> rmsd A :11-125 ref [struct0] perres perresout PRMS.dat range 11-125 perrescenter perresmask &!.H,N,CA,HA,C,O
>> run
>> xmgrace PRMS.dat
>>
>> Obviously there is something wrong with the script because instead of producing an x-axis with residue numbers, the x-axis represents frame number.
>>
>> I’d appreciate any suggestions on how to improve the script to generate per-residue RMSD averaged over the trajectory time.
>>
>> 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 Tue Aug 18 2015 - 10:00:04 PDT
