Thanks so much Daniel...That worked! It's exactly what I needed...
Steve
-----Original Message-----
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Friday, October 16, 2020 12:32 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] rms(d) or (f) per residue
Hi,
On Fri, Oct 16, 2020 at 1:22 PM Seibold, Steve Allan <stevesei.ku.edu> wrote:
>
> Thanks for your response...
> I tried the following:
> >rms reference :1-548 perres perresout file.dat perresavg
You need to specify a file name. Not sure why that didnt kick back an error. You probably want something like: 'rms reference :1-548 perres perresout file.dat perresavg avgfile.dat'
>
> This gave an output file containing 6 column and hundreds of rows with half contain the residue name and number (e.g. MET:12 THR:13 TYR:14 ect...) followed by rows containing the rms values 3.341 2.945 1.381 etc...).
>
> The output look like:
>
> MET:12 THR:13 TYR14 etc........
> ..............................................
> ..............................................
> 3.341 2.945 1.381 etc..........
> ..............................................
> ..............................................
>
>
> My be my format shown above is incorrect?
>
> Thanks for your help...
>
> Steve
>
> -----Original Message-----
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Friday, October 16, 2020 12:06 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] rms(d) or (f) per residue
>
> Hi,
>
> The file produced by 'perresavg' will have the average and standard deviation of each residue specified - maybe that is closer to what you want?
>
> -Dan
>
> On Fri, Oct 16, 2020 at 12:51 PM Seibold, Steve Allan <stevesei.ku.edu> wrote:
> >
> > Hi
> > I am trying to do something simple but am having a difficult time getting cpptraj to write out the dat file properly. I want to produce an output file containing two columns. The "x" coordinate containing residue numbers 1-548 and the "y" coordinate containing the rms(f or d) values for each residue (numbered 1-548). Is this possible? I have tried the "byres" and the "perres" command but neither is working for me...
> >
> > Thanks, Steve
> > _______________________________________________
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> > ts
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> > i%
> > 40ku.edu%7Cf2320147a7704c64611f08d871f5e0d0%7C3c176536afe643f5b96636
> > fe
> > abbe3c1a%7C0%7C0%7C637384648145822476&sdata=OF4x%2BIFhTcT%2BPYmf
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>
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Received on Sat Oct 17 2020 - 05:30:02 PDT
