Hi,
Unless you have added the original PDB residue numbers into your Amber
topology using parmed, they are not available for use. You will need
to add the info using parmed's 'addPDB' command. Alternatively you
could manually set the proper residue numbers using the cpptraj
'change' command, e.g.
change oresnums of :1-10 min 3 max 12
Will change the "original" residue numbers of the active topology for
residues 1 to 10 to 3, 4, 5, etc. Hope this helps,
-Dan
On Tue, Mar 14, 2023 at 10:58 AM Roy, Rajarshi <roy212.purdue.edu> wrote:
>
> Hi,
>
> It appears that I can currently print the residue number according to my specifications. However, my concern is how to print the original residue number rather than the residue number. According to the AMBER residue information, the "#Res" value indicates the residue number, while the "#Orig" value indicates the original residue number. I require the "#Orig" value in my rmsf output file instead of "#Res". Is it possible to obtain this using a single command, or will I need to use a separate set of commands?
> Thank you for your understanding and time.
>
> Sincerest thanks
> Rajarshi Roy
> Post Doc Research Associate
> Purdue University
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Sunday, March 12, 2023 9:25 AM
> To: Roy, Rajarshi <roy212.purdue.edu>
> Cc: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Request for Assistance with AMBER Output File for RMSF Analysis
>
> ---- External Email: Use caution with attachments, links, or sharing data ----
>
>
> Hi,
>
> That's an old version. Try updating to the latest AmberTools or GitHub
> version (https://github.com/Amber-MD/cpptraj) and try again. A brief
> test seems to work for me:
>
> parm ../tz2.parm7
> trajin ../tz2.nc
> align !.H= first
> atomicfluct :4-8&!.H= byres out fluct.dat
>
> $ cat fluct.dat
> #Res AtomicFlx
> 4.000 4.8362
> 5.000 5.3119
> 6.000 5.2553
> 7.000 3.8453
> 8.000 5.3664
>
> -Dan
>
> On Fri, Mar 10, 2023 at 3:30 PM Roy, Rajarshi <roy212.purdue.edu> wrote:
> >
> > Hi,
> >
> > I am using V5.1.0 (AmbetTools V21.12) of cpptraj.
> >
> > Here is my code snippet:
> >
> > rms first mass @N,CA,C
> > atomicfluct out $out_path/rmsf_CA_$file.dat :;$N_res.CA byres
> >
> >
> > Sincerest thanks
> > Rajarshi Roy
> > Post Doc Research Associate
> > Purdue University
> >
> > ________________________________
> > From: Daniel Roe <daniel.r.roe.gmail.com>
> > Sent: Friday, March 10, 2023 3:26 PM
> > To: Roy, Rajarshi <roy212.purdue.edu>; AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] Request for Assistance with AMBER Output File for RMSF Analysis
> >
> > ---- External Email: Use caution with attachments, links, or sharing data ----
> >
> >
> > Hi,
> >
> > What version of cpptraj are you using, and what is in your input script?
> >
> > -Dan
> >
> > On Fri, Mar 10, 2023 at 3:21 PM Roy, Rajarshi via AMBER
> > <amber.ambermd.org> wrote:
> > >
> > > Dear AMBER users and developers,
> > >
> > > I am writing to request assistance regarding the output file of the RMSF analysis. Specifically, I would like to print the original residue numbers in the file, but despite using :; to select the residues, the file is still printing residue numbers starting from 1. I would greatly appreciate any guidance or suggestions on how to resolve this issue.
> > >
> > > Thank you in advance for your help.
> > >
> > > Sincerest thanks
> > > Rajarshi Roy
> > > Post Doc Research Associate
> > > Purdue University
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Mar 15 2023 - 07:30:03 PDT
