I want to calculate number of close contact and contact area calculation for a receptor-ligand interaction. I had performed MD using NAMD.
I tried to search any VMD script for this, but not successful, could any one suggest me how to proceed for this.
Hi,
You could try using the 'nativecontacts' command in CPPTRAJ, which is freely available as part of AmberTools. This command defines native contacts using a reference structure and simple distance cutoffs. It will also report the number of native and non-native contacts. For example, if I wanted to examine contacts between heavy atoms in a residue named NDP and residues 1 to 268, using the first frame to define native contacts and a distance cutoff of 3.0 Ang. I could use a script like:
parm topology.psf
trajin trajectory.dcd
nativecontacts :NDP&!@H= :1-268&!@H= writecontacts contacts.dat out numcontacts.dat first distance 3.0
Hope this helps,
Dear Chiara,
Thankyou for the reply my system is about 136000 atoms, it will be great help if you provide the sample scripts to me, email [email protected].
Thanks
Hi,
You could try using the 'nativecontacts' command in CPPTRAJ, which is freely available as part of AmberTools. This command defines native contacts using a reference structure and simple distance cutoffs. It will also report the number of native and non-native contacts. For example, if I wanted to examine contacts between heavy atoms in a residue named NDP and residues 1 to 268, using the first frame to define native contacts and a distance cutoff of 3.0 Ang. I could use a script like:
parm topology.psf
trajin trajectory.dcd
nativecontacts :NDP&!@H= :1-268&!@H= writecontacts contacts.dat out numcontacts.dat first distance 3.0
Hope this helps,
There is this CAD-score (contact area difference) tool available from Olechnovic & Venclovas http://bioinformatics.ibt.lt/cad-score/theory. It is geared towards the contact area difference between two conformations, but the absolute data you are seeking is there in a some sort of auxiliary file.
Thankyou Visvaldas for the reply related to contact area calculations.
I recommend ContactFreq in VMD:
load the simulation trajectory into VMD, after type "source ContactFreq.tcl" in the tkconsole
type contactFreq "selection for protein" "selection for ligand" to get the residue based contact frequency output to the tk window. Here assume contact is defined as < 4 angstrom distance. Check script for other options.
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