I want to make index file of some atoms with similar name. What is the easiest way to do this in gromacs?
If you simply want an index file with static selections, using make_ndx as follows would be the easiest.
$ make_ndx -f conf.pdb (or topol.tpr) -o index.ndx
> a C1 C2 C3 C4 C5 ... C20
> q
Another simple way to do the job is using VMD. Select the atoms you want and then output their atom ids.
ps: The powerful feature of gmx select is supporting dynamic selections, such as water within 0.5 nm of protein.
Hope it helps.
Cong Guo how can I compute the number of water molecules within 5 angstrom of two residues of a protein along the trajectory (lipid bilayer)?
Thanks and regards
Budheswar
The command gmx select can do the job.
gmx select -f *.xtc -s *.tpr -os size.xvg -oi index.dat -select 'group X and within 0.5 of group Y'
It dynamically selects atoms in group X within 0.5 nm of group Y. In your case, group X = water molecules or water oxygen atoms more specifically, group Y = two residues (for example residue 1 2). Then the following command will work.
gmx select -f *.xtc -s *.tpr -os size.xvg -oi index.dat -select 'name OW and within 0.5 of (residue 1 2)'
The number of OW atoms is saved in size.xvg. The list of the selected OW atoms is saved in index.dat.
Cong Guo ..Madam thanks a lot for your quick and prompt reply. I have tried with the following command its shows following error..How can I do selection..?
gmx select -f md_fit.xtc -s md.tpr -os size.xvg -oi index.dat -select
'name OW and within 0.5 of (residue 263 & chain B && residue 366 & chain C)'
In command-line option -select
Invalid selection 'name OW and within 0.5 of (residue 263 chain B &&
residue 366 chain C)'
syntax error
With the selection ‘residue 263 & chain B && residue 366 & chain C’, NO atoms are selected.
First, '&&' should be 'or'.
Second, the keyword 'residue' is different from 'resid’. If there are N residues in your system , residue ranges from 0 to N-1. I guess you want to select the 263rd residue in chain B and the 366th residue in chain C. Assume their correct residue indexes are i and j. The right selection sentence should be 'name OW and within 0.5 of (residue i j)'.
@Cong Guo Hello, I tried your method for my system but i am not getting the correct numbers. I am currently trying to count the number of ions between two groups. Each group has 16 atoms which i grouped under one name. I used the following command but the numbers i am getting is way above what i visualized in VMD gmx select -f md.xtc -s md.tpr -os Ca.xvg -oi index.dat -select 'name Ca and within 1 of (resname 1 2)'
where 1 and 2 are the two groups and Ca is the ion between these two.
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