[gmx-users] Ligand-protein free binding energy is become positive
I’m using MM-PBSA on gromacs to calculate free binding energy of some ligands into K-Ras (pdb-ID: 4epy). To validate MD simulation protocol and to setup a rational threshold for evaluating the results, the co-crystal ligand was considered as the reference ligand. Results showed that free binding energy of reference ligand and my selected ligands have positive quantities. Due to the fact that we are sure about the binding of reference ligand into the binding pocket. How can we describe positive value of the free binding energy? Results of MM-PBSA calculation for reference ligand is as below: Reference ligand: van der Waal energy =-166.208 +/- 32.482 kJ/mol Electrostattic energy= 144.473 +/- 15.430 kJ/mol Polar solvation energy = 529.921 +/- 91.034 kJ/mol SASA energy = -18.937 +/-3.458 kJ/mol SAV energy = 0.000 +/-0.000 kJ/mol WCA energy = 0.000 +/-0.000 kJ/mol Binding energy = 489.143 +/- 46.438 kJ/mol -- 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.
[gmx-users] Umbrella sampling
Hi everybody I’m trying to do Umbrella Sampling by using Justin’s tutorial. Everything is ok but some aspects of the procedure remain a bit unclear to me. Why don’t we need to do NVT equilibration before first MD? And why pull codes are applied during NPT equilibration of selected windows or extracted frames? -- 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.
[gmx-users] How to add a repulsive harmonic potential through define virtual atom?
Hello dear GMX users I want to predict the probability binding of ligand to protein by unguided simulation. But when I increased concentration of ligand in the simulation box, the ligands has aggregated. So I decide to add repulsive potential between some atoms of ligands. I had search the archive of GMX-User mailing list and saw this question: How to add a repulsive harmonic potential?(1) , and read its answers. Finally according to the Justin’s Solution I defined one new ATOM in [atomtype] section and placed it in the [atoms] section of my ligands topology file (lig.itp). Then I defined the added atom as virtual atom in [virtual_sitesn] section. Then I create a new topology file (ligand-parameter.itp) that includes [atomtype] section of ligands (has cut from ligand topology files) and [nonbond_params] section. Also I added coordination of these new atoms in my complex coordination file (Conf.pdb). When I run command gmx mdrun -v -deffnm em got this error: Software inconsistency error: The mass of a vsiten constructing atom is = 0. Can anyone help me to fix this error? Log file of what I do is here (log) (Files are in download links) 1- https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096469.html Download links : http://d01.megashares.com/dl/Jt8d7PZ/lig.itp http://d01.megashares.com/dl/LguyLcH/ligand-parameter.itp http://d01.megashares.com/dl/FHhKyVe/conf.pdb http://d01.megashares.com/dl/aIEDwDN/log -- 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.
[gmx-users] (no subject)
Hello dear friends I want to simulate a Ligand-Protein complex in GROMACS by using amber forcefield https://www.google.com/search?q=forcefieldnewwindow=1sa=Xbiw=1366bih=657tbm=ischtbo=usource=univei=WEaQVYH_AoWdsgH06q6ICgved=0CE4QsAQ and need essential MDP files. Can anyone provide me that files? -- 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.
