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
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--
-------------------------
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
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Received on Tue Feb 21 2017 - 07:00:02 PST
