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
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Received on Fri Mar 03 2017 - 07:30:02 PST
