Hello everyone. I am using Gromacs for protein-ligand MD. For detailed analysis i need to plot contact maps between protein side chain heavy atoms and heavy atoms but using gmx mdmat I was able to generate intrapeptide contacts only. I have prepared index file of ligand containing its heavy atoms but even after using it, the result was same. i.e. contactmap.xpm contains protein residues only. there are 40 residues in protein. PDB ID is 1IYT and there are 23 heavy atoms in ligand
YASARA can be used to do this. For 2D contact descriptions, COOT and LIGPLOT work quite well.
Hi,
did you prepare your index group properly? it sounds unusual that by making index of one group, you are unable to get the desired results. Another possibility, just count the number of atoms in your index group and match them with *.xpm file. It is possible that your index contains only heavy atoms of protein+ligand, but you are focusing on the total number of atoms in xpm file.
Best.
I also used LIGPLOT for small-molecule protein contacts
protein-protein contacts are to do with UCSF Chimera (Function "find contacts")
I think this is also working with small molecules protein
@ Dr. Ayaz Anwar, The ligand heavy atoms are 29 but i am getting residue-residue contact map as a result even after providing correct index file. And Sir, can you please elaborate the second part of your answer: It is possible that your index contains only heavy atoms of protein+ligand, but you are focusing on the total number of atoms in xpm file. How to edit the *.xpm to obtain index atoms only? Using simple text editor?
I am attaching my *.xpm .Please have a look
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology