No. pull_ncoords defines how many biasing potentials there are. Each pull_coord*_dim specifies the dimensions in which a given bias acts.
Hi,
Thank you very much for the reply.
My aim is to calculate delta G of my protein ligand complex through umbrella sampling. I am following your tutorials with the required modifications.
I have run the pull code for 100 ps.
with pull-coord1-dim = N Y Y, thus setting a distance in the y-z plane.
In order to iteratively call gmx distance, you have written a perl script which generates summary_distances.dat. After running the perl script, I got the following error
readline() on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $distance in concatenation (.) or string at distances .pl line 30.
Could you please tell, where to fix the mistake, as I am a beginner?
The Perl script is designed for the tutorial specifically, so you'll have to modify it to suit your needs. The error indicates that gmx distance is failing for some reason, and you'll have to invoke it manually to see why and figure out the proper syntax for your system.
Why are you only applying a bias in the Y-Z plane for a protein-ligand complex? That's rather odd; normally all dimensions should be considered for such systems.
Hi,
I have another query. In protein-ligand complex tutorial, you have a ready made .pdb file of the docked complex (cleaned version). Using which software did you obtain the docked complex? Using Auto Dock Tools? When I used the PRODRG server, it added two hydrogen atoms to nitrogen on its own. How to avoid this?
The tutorial uses a structure from the PDB.
PRODRG makes guesses as to protonation states; please refer to the PRODRG FAQ on how to control this; it is explicitly described.
Hi,
The calculations ran for a long time (for pull code 500ps).
But, it gave the message
Distance between pull groups 1 and 2 (3.219335 nm) is larger than 0.49 times the box size (3.284899).
You might want to consider using "pull-geometry = direction-periodic" instead.
Should I increase the box size?
If you're unclear about basic settings for different ensembles, go back and do some simple tutorial material. You've omitted the pull settings, which are important if you're applying a biasing potential.
Note that using "direction-periodic" OR using NVT such that the box size does not vary are possible solutions. You don't have to do both. Also note that using NVT as the ensemble for sampling means you get a Helmholtz free energy, not a Gibbs free energy.
Hi,
In NPT ensemble, I ran the code for 20 ps (for trial purposes, in xy plane) and obtained sumarry_distances.dat by modifying the perl script.
How to extract information from this?
0 0.675
1 0.723
2 0.711
3 0.721
4 0.767
5 0.730
6 0.745
7 0.748
8 0.753
9 0.723
10 0.785
11 0.795
12 0.782
13 0.720
14 0.752
15 0.714
16 0.751
17 0.776
18 0.755
19 0.785
20 0.739
Second column represents the COM separation distances. See if the COM distance increases constantly. If does not then the pulling is not happening properly, as it seems in this case to me.
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