[gmx-users] Non-covalent interactions in the protein-ligand systems

James Starlight jmsstarlight at gmail.com
Sat Oct 22 18:14:10 CEST 2011

Dear Grpmac's Users!

Recently, I've done Protein-ligand tutorial consisted of simulation of the
lysozyme with the ligand.

I have some questions about analysisng of the results, in particular I want
to analyse all non-covalent interactions in that system

1) First off all I've tried to analyse potential H-bonds in that system.
I've analysed very short 0.5nm trajectory since my simulation have not been
completed yet so I've obtained

Found 256 donors and 481 acceptors
Will do grid-seach on 18x18x13 grid, rcut=0.35
Reading frame     200 time  400.000
Found 2 different hydrogen bonds in trajectory
Found 2 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
- Reduced number of hbonds from 2 to 2
- Reduced number of distances from 2 to 2
HB lifetime = 4.03 ps

>From that information I've found that 2 h-bonds have been emerged during 0.5
simulation with their lifetime 4ps.

Firstly, during analysis of the *-num*
hbnum.xvg<http://manual.gromacs.org/current/online/xvg.html>file I
have not found presence of the two above bonds (this graphs was
consisted of the time on X and strange scale measured from 0 to 1 on Y). How
that graphs might be interpreted?  By the way what are the typical time of
the arising of the h-bonds in such systems and how it could be dependent on
the background factors  ?

Than I've found that all hbonds are calculated in the scope of the cutt-off
distance ( from above log I've found that such distance is the 0.35 isnt it?
) How I can define such cutoff rad? In my MDF file I've found only
parametries for the cuttoffs for the Electrosatics as well as for the vdv
contacts. Does the cut off for the H-bond was calculated on the combination
of the above values?

2) Also I want to investigate posible contributions of the others
non-covalent contacts in my protein-ligand system. What gromacs programs
might be used for the calculation of the electrostatics and the hydrophobic
contacts by the analogy of the ussage of the g_hbond?

Thanks for your help,

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