I want to analyze the deviation of salt bridge length in different temperature gradient of a protein. I have run the protein simulation for 100ns, where I have got 100 different pdbs. But I need a single pdb from a specific temperature simulation for the analysis. So, my question is how can I get the specific pdb for the analysis?
I have tried PCA from where I get an average pdb for a specific temperature. But the average pdb (attached below) contains lots of rotamers or conformers for every residues of the protein. In this structure, the backbone and side chain of the residue become totally changed from where salt bridge analysis is very difficult. In average pdb, the atoms of the side chain become collapsed together.
I have run simulation of the protein in GROMACS. So, please help me how can I proceed further and find the pdb on which I can do the analysis.
You can test in this page, may be that this site generate a single PDB. Regards
I'd say that you don't really need a single PDB from each temperature run. What you may need is a single/average salt bridge length for each temperature - in that case, just calculate the length od the salt bridge in those 100 different PDBs from each single run, and take an average value.
It may be, however, interesting to take a look at the dynamic properties of this particular salt bridge over the course of the MD. Even from a limited number of snapshots (100 in your case) you can get not only the average, but also the min/max values (range), median, mode and other statistical descriptors, that might tell you more about this system.
Hi Manish. Let me tell you what I have here that maybe could help, maybe I misunderstand what you need.
I made a database in MySQL with proteins from pdb.org till a specific resolution. So I have here the PDB, the temperature, pH and the atoms position. So, if you want we can just make a SELECT on the database for specific temperature and amino acid, atoms, to give you the list of distances.
If you prefer, you can also download the database from here.
http://w.a00s.com/fy/proteinas.zip
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