Distance calculation between four different protein residues and the ligand molecule as a function o

User discussions
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1

GROMACS version:
GROMACS modification: Yes/No
Here post your question I am seeking some suggestions or help on how to find the distance between the different protein residues and ligand molecules as a function of time. I am seeing some suggestions regarding making index file of all the four residues of the protein and group it with the ligand but it did not work for me. Also for the index file do I consider the em. gro file or the output trajectory file (.xtc, or center.xtc or fix.xtc)

As I can see some other people also having trouble with the same issue a detailed explanation may also help others too.

Thank you.

2

What did you do? What happened?

The atom order never changes, so it is irrelevant which coordinate file you use (you cannot use trajectories for input to make_ndx).

3

I followed this command:

gmx_mpi distance -f md.xtc -s md_0_10.tpr -n md_0_10.ndx -oav distave.xvg -oall dist.xvg -oxyz distxyz.xvg -oh disthist.xvg -oallstat diststat.xvg -select com of group "22" plus com of group "13" -tu ns -dt 50

The error says that there are no such groups:

Error in user input:
Invalid command-line options
Unknown command-line option -selectcom of group “22” plus com of group
“13”

4

Selection strings need to be enclosed by single quote marks.

gmx_mpi distance -f md.xtc -s md_0_10.tpr -n md_0_10.ndx 
-oav distave.xvg -oall dist.xvg -oxyz distxyz.xvg -oh disthist.xvg 
-oallstat diststat.xvg -select 'com of group "22" plus com of group "13"' 
-tu ns -dt 50
5

Hello Dr. Lemkul,
Thank you for the response. Its now showing a new error (mentioned below):

Invalid index group reference(s)
Cannot match ‘group “22”’, because no such index group can be found.
Cannot match ‘group “13”’, because no such index group can be found.

6

Group numbers are specified without quotation marks (which are used for group names).

7

Thank you @jalemkul, the command worked, but as an output, I am getting all blank graphs and histograms.

But I am also getting the output numbers (mentioned below):

Analyzed 1 frames, last time 10000.000
com of group 22 plus com of group 13:
Number of samples: 1
Average distance: 8.01073 nm
Standard deviation: 0.00000 nm

I am a bit confused here. What am I doing wrong here? My motive is to select 4 residues from my protein of interest and find out the distance change (change in trajectory) of my ligand over the course of the simulation. Then plot the distance as a function of time.

8

Apparently whatever you’re analyzing has one frame, so you’re not going to get a time series. If you have a multi-frame trajectory, you’ll get the output you want as a function of time. I have no idea what your groups are, but if you want four distance time series, you need to have the four residues of interest in their own groups and compute each COM distance of interest separately.