Re: [gmx-users] Energy minimization result problem
Hi, Proteins do not have a single holy structure, nor is any given quantity of MD going to find it, if it exists. Neither is there a single metric of suitability - backbone strain as measured by Ramachandran plot deviations could easily be the result of accommodating worse problems while stuck in a local minimum. You can get zero deviations by unfolding the whole protein, but that isn't going to tell you anything. Or the deviations could be good things, because parts of your structure are atypical, but healthy. Mark On Apr 13, 2014 9:52 AM, neha_bharty nehabharty...@gmail.com wrote: Hello Justin Lemkul Thank you very much for your reply. I also preformed MD for 15 ns. After MD I check my protein model with Ramachandran Plot using Online Procheck server. But the result was same as after energy minimization. The residues which were present in allowed region was again less than that of previous protein. As I am new in gromacs I don't have much idea. In my view I guess after energy minimization and MD the residues which were present in allowed region of Ramachandran plot should be increases. And if it decreases it means the previous model is better. Is there any other way to check my protein model is better after energy minimization and MD or not?? If require I can also send the .mdb file I have used for MD. -- View this message in context: http://gromacs.5086.x6.nabble.com/Re-Energy-minimization-result-problem-tp5015793p5015811.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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. -- 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.
Re: [gmx-users] Energy minimization result problem
Hello I am new user of gromacs. I am using gromacs 4.6.3 I wanted to minimize the energy of a protein. Before energy minimization the prockeck result for Ramachandran plot was 89% in allowed region but after energy minimization the result become worse i.e. 87%. I was performing energy minimization to refine the model. But the model become worse after that. I Model the protein using homology modeling and needed it for docking I am also doing it with different protein molecules but again the same problem occurs. I don't know that its normal or there is problem with my parameter or force field. I am also mentioning the detail of my energy minimization. The details are: Force Field Used: CHARMM27 all-atom force field Water Model: TIP3P em.mdp file is: ; VARIOUS PREPROCESSING OPTIONS = title= cpp = /lib/cpp include = define = -DFLEXIBLE ; RUN CONTROL PARAMETERS = integrator = steep ; start time and timestep in ps = tinit= 0 dt = 0.002 nsteps = 15000 ; ENERGY MINIMIZATION OPTIONS = emtol= 10 emstep = 0.1 nstcgsteep = 1000 coulombtype =pme nstenergy =10 Please help me out for this. -- View this message in context: http://gromacs.5086.x6.nabble.com/Re-Energy-minimization-result-problem-tp5015793.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.
Re: [gmx-users] Energy minimization result problem
On 4/11/14, 7:47 AM, neha_bharty wrote: Hello I am new user of gromacs. I am using gromacs 4.6.3 I wanted to minimize the energy of a protein. Before energy minimization the prockeck result for Ramachandran plot was 89% in allowed region but after energy minimization the result become worse i.e. 87%. I was performing energy minimization to refine the model. But the model become worse after that. That's not a huge change, nor is energy minimization rigorous enough to fully refine a model. EM will probably optimize the side chains pretty well, but the backbone may require actual MD simulation to sample better conformations. The changes that take place during EM are typically very small. I Model the protein using homology modeling and needed it for docking I am also doing it with different protein molecules but again the same problem occurs. I don't know that its normal or there is problem with my parameter or force field. I am also mentioning the detail of my energy minimization. The details are: Force Field Used: CHARMM27 all-atom force field Water Model: TIP3P CHARMM36 may be a better option. The recalibration of the CMAP terms could be relevant here. See http://mackerell.umaryland.edu/CHARMM_ff_params.html to download the force field files. -Justin em.mdp file is: ; VARIOUS PREPROCESSING OPTIONS = title= cpp = /lib/cpp include = define = -DFLEXIBLE ; RUN CONTROL PARAMETERS = integrator = steep ; start time and timestep in ps = tinit= 0 dt = 0.002 nsteps = 15000 ; ENERGY MINIMIZATION OPTIONS = emtol= 10 emstep = 0.1 nstcgsteep = 1000 coulombtype =pme nstenergy =10 Please help me out for this. -- View this message in context: http://gromacs.5086.x6.nabble.com/Re-Energy-minimization-result-problem-tp5015793.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
