I have performed MD simulation of protein-peptide complex for 300ns time interval and write frames at every1ns. I ran the simulation in triplicates. When I was extracting pdb files at different time interval after performing MD. At few instances, COOH group of GLUTAMIC ACID is showing unusual conformation. These unusual conformation are found in all triplicates but at different time frames.
There were clashing at some point of time such as at 50ns the COOH group is showing clash but it is normal at 51ns.
Such type of abnormalities, I have found in many places in protein simulation.
Please let me know the exact reason of this abnormality.
I am not able to understand the reason.
Thanks
Shipra
First, what MD program are you using? Which force field? You say you have found such abnormalities in many places in protein simulation (I guess you are talking about other simulations than these ones?), so that makes me think that you might be using an incorrect version of a force field? Are these abnormalities always related to the COOH of glutamates?
Then, what do you mean by an "unusual" conformation of the COOH group? I imagine you mean there is something wrong with the geometry, but I cannot picture what would it be without more information.
Lastly, 1 ns is a very large interval for writing frames. You are certainly missing a lot of information of what is happening in your simulation. For example, that "clash" at 50 ns that is solved at 51 ns, how did that happen? Also, in that frame at 50 ns, the COOH is in an "unusual" conformation? If so, the conformation is then normal at 51 ns?
Dear Almudena,
I am using amber99sb-ildn.ff force field of Gromacs-5.0.4-intel program for simulations. I ran one simulations in triplicates (one protein in triplicates for 300ns). Theses abnormalities are related to dihedral angles and bond length of GLU45 and GLU53 only.
If force field parameters are wrong, than how to resolve the problem.
Thanks.
Shipra
Why are you not using charged glutamates, ie CO2- instead of COOH?
Also, you need to run an energy minimization of each of these snapshots, and the unusual geometries should be fixed.
Theses abnormalities are related to dihedral angles and bond length of GLU45 and GLU53 only.Can you make a plot of angle and dihedral of these residue with time and pest here. I doubting it may the case of broken molecules due to pbc.
I agree with Almudena, 1 ns is a very long time between frames - at least for the initial period. Also, are you properly minimizing the system before the simulation?
Mrs/Miss Gupta,
MD is not so suitable for conformational optimization of aliphatic chain structures. It would be better to perform MMX (X = 2 or 3). Please find as attachment MD and MM2/3 of glutamic acid.
Ms Ivanova,
It seems like MMX would be much more resource intensive for a protein-ligand complex simulation as compared to plain MD? Perhaps even prohibitively so?
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