I want to perform molecular dynamics simulation of my protein which is modified for the oxidation of a particular amino acid which has been proved by mass spectrometric analysis. Can any one suggest how I can deal with the nomenclature of the modification of structure files while performing MD simulation for the smooth running. Are there any tutorials available for post translated modified proteins to perform simulations?
Standard protein parameters are available. If your structure has changed (it seems that you have added some oxygen molecules) than you need to build parameters for the modified section. Generation of parameter is not that easy. There are lot's of discussion on researchgate, charmm and namd forum.
Thanx a lot Jahiruddin.. ok i will go through the discussions as you have mentioned above. Also i would like to know about the standard protein parameters, if you have any link or pdf document..can you plz attach here.. thank you..
This is the link. These force field files will work with CHARMM and NAMD. For Amber an Gromacs the files are available in their respective websites. NAMD and Gromacs are free. Amber and CHARMM you need to buy. It is better to use NAMD. Very easy to install. So easy to use. Tutorials are the best.
http://mackerell.umaryland.edu/charmm_ff.shtml
http://www.ks.uiuc.edu/Research/namd/
If for the problem is enough simplistic nonstandard parameters, you can use the universal force fields, such as DREIDING. For example thus do Abalone in its "ad hoc" model (default). However, as it was not a simple covalent model, accurate charges are necessary. Simple and quite adequate charge model is RESP (from AMBER).
http://www.biomolecular-modeling.com/Abalone/index.html
If you have access to the AMBER MD package, you can try this tutorial:
http://sf.anu.edu.au/~vvv900/amber-tutorial/1cgh-nonstandard/index.html
it is a bit tricky, but if you follow the steeps carefully, everything is well explained.
try PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues (PTMs, non-natural residues, D-amino acids etc). [http://osddlinux.osdd.net/raghava/pepstrmod/nat_ds.php]
article link : http://www.biologydirect.com/content/10/1/73
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