Thanks!
I'll try it after this weekend.
Best regards
Karolina
2017-03-03 16:02 GMT+01:00 Daniel Roe <daniel.r.roe.gmail.com>:
> Hi,
>
> FYI the latest GitHub version of cpptraj has a new keyword for
> 'atomicfluct byres', 'pdbres', which will use original PDB numbers in
> the output (assuming you use a PDB with this info as your topology).
>
> -Dan
>
> On Tue, Feb 21, 2017 at 9:30 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> > By default recent versions of cpptraj (definitely 16+) will use
> > information from the PDB such as original residue number, chain ID,
> > etc only when writing in the PDB format (e.g. from using
> > trajout/outtraj/crdout etc). There is currently no mechanism for
> > making cpptraj use this information in non-PDB output such as that
> > from atomicfluct or in atom mask selection. It could potentially be
> > useful to add in the future. I have opened an issue on GitHub related
> > to this (https://github.com/Amber-MD/cpptraj/issues/459) and will try
> > to get to it when I get a chance.
> >
> > -Dan
> >
> > On Tue, Feb 21, 2017 at 8:54 AM, Karolina Mitusińska (Markowska)
> > <markowska.kar.gmail.com> wrote:
> >> Dear Amber Users,
> >>
> >> I would like to know, when does cpptraj use the residue number
> information
> >> from the original pdb file?
> >> I have found this mail: http://archive.ambermd.org/201611/0140.html and
> >> after I used the new topology file to generate RMSF plot I saw that
> cpptraj
> >> won't use the original pdb file residue number.
> >> How to make it use those informations?
> >>
> >> For example:
> >> if I type:
> >>> resinfo :189-196
> >> #Res Name First Last Natom #Orig #Mol
> >> 189 TYR 3092 3112 21 221 0 A
> >> 190 TYR 3113 3133 21 222 0 A
> >> 191 VAL 3134 3149 16 223 0 A
> >> 192 GLN 3150 3166 17 224 0 A
> >> 193 GLY 3167 3173 7 225 0 A
> >> 194 GLY 3174 3180 7 226 0 A
> >> 195 ASP 3181 3192 12 227 0 A
> >> 196 TRP 3193 3216 24 228 0 A
> >>
> >> I want to have the numbers from the #Orig column instead of #Res in my
> >> output file for RMSF.
> >>
> >> Best regards
> >> Karolina Mitusińska
> >> PhD student
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe
> > Laboratory of Computational Biology
> > National Institutes of Health, NHLBI
> > 5635 Fishers Ln, Rm T900
> > Rockville MD, 20852
> > https://www.lobos.nih.gov/lcb
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Mar 03 2017 - 10:00:03 PST
