On 7/3/17 4:20 AM, Tushar Ranjan Moharana wrote:
Hi all, I want to know the contribution of various amino acid side chain in complex that composed of 2 proteins. I used GROMOS53a6 forcefiel for the simulation. All parameters are as recommended by the concerned paper. I made separate index groups for each amino acid side chain and the proteins. I calculated Coulomb and LJ interaction using gmx energ between the amino acid and the interacting protein. Following are few results, I obtained: Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------ ------------------- Coul-SR:161TYR-Protein_B -74.0397 1.9 17.8364 8.11782 (kJ/mol) LJ-SR:161TYR-Protein_B -49.535 1.5 10.2926 2.73416 (kJ/mol) Coul-14:161TYR-Protein_B 0 0 0 0 (kJ/mol) LJ-14:161TYR-Protein_B -1.20657 0.088 0.533195 0.474622 (kJ/mol) where Protein_B is the other protein in the complex. I have following doubts. 1) Energy I obtained looks too high to me. Is everything correct? I searched for information but couldn't get much, so don't know what should be the ideal values. Results might be correct but I am not sure.
I don't know how you're making this assessment. Your numbers look to be of reasonable magnitude, though I'm not sure how you have a 1-4 term between different protein units. Check your index groups.
2) How can I calculate kinetic energy of the amino acid side chain? gmx traj or energy(after saving only desired atoms in the trajectory) which one will be more meaning full?
You can do it either way, but I would argue that neither is actually meaningful. -Justin
Kindly help me at least in the first question. Any kind of informations/suggestions are most welcom. Thanks for your valuable time and efforts. "A society with free knowledge is better than a society with free food"
-- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
