make_ndx "AND" keyword seems broken - Redmine #1976
Archive from user: Chris Neale
I have tried using the ‘AND’ keyword, which is noted in the gmx make_ndx -h output. Indeed, the word “AND” replaces the ampersand in the index group in this case. However, the selection seems broken to me. Details are below. Specifically, with the ‘&’ between selection of one atom name and one residue number, I get one atom in the group, as expected. However, when I use the ‘AND’ keyword, “r” seems to get promoted to “R” and then (for this or other reasons) the selection of one particular residue is not honored.
NOTE: same behaviour if using “AND” or “and”
In the following, note that there are 128 lipids and that each lipid has a single atom names C316. Therefore selecting a single residue and a name of C316 should give a single atom.
$ echo -e "aC316 AND r1 \n aC316 & r1 \n q \n" | gmx make_ndx -f start.gro -o rdf.ndx
:-) GROMACS - gmx make_ndx, VERSION 5.1.2 (-:
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GROMACS: gmx make_ndx, VERSION 5.1.2
Executable: /home/cneale/exec/GROMACS/exec/gromacs-5.1.2/serial/bin/gmx
Data prefix: /home/cneale/exec/GROMACS/exec/gromacs-5.1.2/serial
Command line:
gmx make_ndx -f start.gro -o rdf.ndx
Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are: 128 Other residues
There are: 6396 Water residues
There are: 34 Ion residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
0 System : 35862 atoms
1 Other : 16640 atoms
2 DPPC : 16640 atoms
3 K : 17 atoms
4 CL : 17 atoms
5 Water : 19188 atoms
6 SOL : 19188 atoms
7 non-Water : 16674 atoms
8 Ion : 34 atoms
9 DPPC : 16640 atoms
10 K : 17 atoms
11 CL : 17 atoms
12 Water_and_ions : 19222 atoms
nr : group ! 'name' nr name 'splitch' nr Enter: list groups
'a': atom & 'del' nr 'splitres' nr 'l': list residues
't': atom type | 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
'ri': residue index
>
Found 128 atoms with names C316 AND R1
13 C316_AND_R1 : 128 atoms
>
Found 128 atoms with name C316
Merged two groups with AND: 128 130 -> 1
14 C316_&_r_1 : 1 atoms
>
###
I did not test the “NOT” or OR" keywords, but they are probably suspect as well.
Thank you,
Chris.
(from redmine: issue id 1976, created on 2016-05-31 by gmxdefault, closed on 2016-06-02)
- Changesets:
- Revision 13e0dc71 by Teemu Murtola on 2016-05-31T19:27:48Z:
Improve make_ndx help text
Clarify the use of boolean operators. The old help text could
incorrectly hint that AND, OR, and NOT would work as keywords.
Add a reference to gmx select that in most cases can serve as a
replacement.
Fixes #1976.
Change-Id: I0284c849c398e5b09569453d7d0f19b9639a6d0c