[gmx-users] LIE calculations

Dear all, Recently i performed 10ns protein ligand simulation and also ran 10ns simulation only for ligand in solvent obtain parameters for g_lie to determine DGBind values. I calculated -Elj -Eqq values from ligand only simulation energy file... this is where im stuck :( -Elj = Lennard-Jones

[gmx-users] LIE calculations

Dear all, Recently i performed 10ns protein ligand simulation and also ran 10ns simulation only for ligand in solvent obtain parameters for g_lie to determine DGBind values. I calculated -Elj -Eqq values from ligand only simulation energy file... this is where im stuck :( -Elj = Lennard-Jones

Re: [gmx-users] Error in ligand coordinate file

has topologies for both ligand and protein.. Please help Nitin On Wed, Aug 8, 2012 at 5:10 PM, Justin Lemkul wrote: > > > On 8/8/12 10:44 AM, sai nitin wrote: >> >> Hi justin, >> >> Ok i will explain more clearly what i really have is protein ligand >&g

Re: [gmx-users] Error in ligand coordinate file

abase So now question how to solve this error..? Can you please suggest some help ? thanks, Nitin On Wed, Aug 8, 2012 at 12:08 PM, Justin Lemkul wrote: > > > On 8/8/12 5:37 AM, sai nitin wrote: >> >> Hi justin, >> >> Thanks for reply now i have ligand corr

[gmx-users] Gromacs to AMBER

Hi all, Can any body know how to take Gromacs trajectories of protein ligand system to AMBER MM-PBSA and further calculate binding free energies using MM-PBSA.. Can any body suggest some tutorials..on this Cheers -- Sainitin D -- gmx-users mailing listgmx-users@gromacs.org http://lists.g

Re: [gmx-users] Error in ligand coordinate file

in rtp entry RA with 32 atoms while sorting atoms. Any help ?? Thanks, Nitin On Tue, Aug 7, 2012 at 11:42 AM, Justin Lemkul wrote: > > > On 8/7/12 5:08 AM, sai nitin wrote: >> >> Hi all, >> >> Recently i performed protein ligand complex simulation my aim is to &g

[gmx-users] Error in ligand coordinate file

Hi all, Recently i performed protein ligand complex simulation my aim is to compute free energy values using g_lie..i came across that to perform g_lie analysis one should two 2 MD simulation one is protein ligand complex simulation (this is done ) used Charmm 27 FF second one is simulate ligand i

[gmx-users] Linear Interaction energy calculations

Dear all, I recently started protein ligand simulation using gromacs my aim is to calculate binding free energies after simulations...I adapted justin tutorial and done 10 ns MD simulations using CHARMM FF and now going through LIE (Linear Interaction Energie method) g_lie in gromacs.. And came

[gmx-users] crude interaction energy using g_energy

Dear all, Recently i performed two 15ns simulation of protein-ligand systems using gromacs of my interest...and using g_energy tool..i calculated crude interaction energy based on short-­‐range energy components Eint = + . ...I got two Eints for two simulations 1) Eint = -51.003 Kcal/mol (firs

[gmx-users] PDB2GMX error in charmm27 Forcefield

Hi all, Im using Charmm27 Forcefield to generate topology of my protein by using PDB2GMX tool but is showing Fatal Error Atom OG is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 178. Can any body tell me how to solve this.

Re: [gmx-users] Protein ligand molecular dynamics simulation

solution for my problem.. Let me know how to solve this ...issue... Cheers, Nitin On Mon, Apr 16, 2012 at 5:03 PM, Justin A. Lemkul wrote: > > > sai nitin wrote: > >> Hi all, >> >> I have done complex (protein + ligand) complex from autodock software >> us

[gmx-users] Protein ligand molecular dynamics simulation

Hi all, I have done complex (protein + ligand) complex from autodock software using this complex im trying to follow http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html tutorial But when i take complex structure directly from autodock result and run PDB

Re: [gmx-users] How to fit ligand in specific site in protein in simulation

sai, > you have to used docked structure to simulation . > 1st convert the dock structure ,that you concider imptortant for > your further study to pdb file (As you used autodock for docking ). > Then perform MD on that structure. > > Have a nice day... > > > On Thu, Apr

Re: [gmx-users] How to fit ligand in specific site in protein in simulation

, Nitin On Thu, Apr 12, 2012 at 10:34 AM, Андрей Гончар wrote: > I think you have to use some special programm for this purpose. > AutoDock, for example, will be the right choice. > > 2012/4/12 sai nitin : > > Hi all, > > > > I am working on protein - ligand molec

[gmx-users] How to fit ligand in specific site in protein in simulation

Hi all, I am working on protein - ligand molecular dynamics simulation using gromacs. I have a protein in which i know binding site which is composed of 5 residues and i have one ligand i have to place this in binding site. Can any body tell me how to do place this ligand to binding site Thanks

[gmx-users] Bad box in protein.gro

Hi all, I recently started molecular dynamics with gromacs performing protein-ligand simulations for my project first i worked out example from justin tutorials on protein ligand system and trying to apply to my protein and ligand. First i generated topology for my protein using pdbgmx and then i

Re: [gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION

Hi arun, You can try swissparam online tool to generate protein and ligand topologies.. Cheers, Nitin -- Sainitin D PhD student Bioinformatics Group Biotechnology Center Technische Universität Dresden Tatzberg 47/49 01307 Dresden, Germany Tel Lab:+49 (0)351 463 40060 -- gmx-users mailing li

Re: [gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION

-ow...@gromacs.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of gmx-users digest..." >> >> >> Today's Topics: >> >> 1. Re: ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION (Justin A.

[gmx-users] Problem during GROMACS 4.5.5 installation

Hi all, I just started learning molecular dynamics analysis of protein-ligand complexes to do this i downloaded GROMACS 4.5.5 and tried to install according to Manual instructions executed following commands.. ./configure make (when i executed this command it is showing following error *** No t