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  • #2083
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Issue created Nov 25, 2016 by Paul Bauer@acmnpvMaintainer

define resid and residue input options to gmx select - Redmine #2083

Archive from user: Chris Neale

The page: http://manual.gromacs.org/documentation/5.1.2/onlinehelp/selections.html has lots of useful information on gmx select syntax. I presume the syntax is the same for some other analysis tools like gmx pairdist -select. However, I am confused about the difference between resid and residue (and then also obviously the same goes for their synonyms resnr and resindex). It seems to me as if resid is the number from the input file (e.g. the pdb file) and residue is determined after doing a fresh renumbering starting at 1 (as one would likely get with resid if one first ran gmx editconf -resnr 1.

I think it would be useful if specific definitions of resid and residue were places on that web page.

Moreover, it is unclear what happens with there are conflicts with residents between the -f a.pdb input and the -s a.tpr input to gmx select. This is important because e.g. gmx select -f my.pdb -on index.ndx fails with an error that “No topology provided, but one is required for analysis” (and that error goes away when one also provides a -s .tpr file as input to gmx select:

…
GROMACS: gmx select, VERSION 5.1.2
Executable: /oasis/scratch/comet/cneale/temp_project/exec/gromacs-5.1.2/exec_serial/bin/gmx
Data prefix: /oasis/scratch/comet/cneale/temp_project/exec/gromacs-5.1.2/exec_serial
Command line:
gmx select -f gromacse.pdb

Reading frame 0 time 1.000 Available static index groups:
Specify any number of selections for option ‘select’
(Selections to analyze):
(one per line, for status/groups, ‘help’ for help, Ctrl-D to end)

resid 1
Selection ‘resid 1’ parsed

———————————————————————————-
Program: gmx select, VERSION 5.1.2
Source file: src/gromacs/trajectoryanalysis/runnercommon.cpp (line 300)
Function: void gmx::TrajectoryAnalysisRunnerCommon::initTopology(gmx::SelectionCollection *)

Inconsistency in user input:
No topology provided, but one is required for analysis

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
———————————————————————————-

(from redmine: issue id 2083, created on 2016-11-25 by gmxdefault, closed on 2017-01-20)

  • Changesets:
    • Revision 17c6b1f0 by Teemu Murtola on 2016-11-29T12:40:54Z:
Additional selection help

- Explain resindex and resnr keywords in selection help.
- Explain how selection-enabled tools treat -s and -f input files.

Fixes #2083

Change-Id: I93e38c46a2bdb35f057688cf29fb3392712c2443
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