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 =
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 =
has topologies for both ligand and protein..
Please help
Nitin
On Wed, Aug 8, 2012 at 5:10 PM, Justin Lemkul jalem...@vt.edu 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
complex from Autodock..I choose best
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 jalem...@vt.edu wrote:
On 8/7/12 5:08 AM, sai nitin wrote:
Hi all,
Recently i performed protein ligand complex simulation my aim is to
compute free energy values
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
, sai nitin wrote:
Hi justin,
Thanks for reply now i have ligand corrdinate file as follows
ATOM 1 N A -13.006 -12.965 -0.251 -0.60 -0.09 N
ATOM 2 C A -13.386 -13.020 1.035 -0.38 0.03 C
ATOM 3 C A -13.037 -14.131 1.869
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
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
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 =
ELJ + ECoul. ...I
got two Eints for two simulations
1) Eint = -51.003
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
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 jalem...@vt.edu wrote:
sai nitin wrote:
Hi all,
I have done complex (protein + ligand) complex from autodock software
using this complex im trying to follow
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
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
,
Nitin
On Thu, Apr 12, 2012 at 10:34 AM, Андрей Гончар gontc...@gmail.com 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 sainit...@gmail.com:
Hi all,
I am working on protein - ligand molecular
, sai nitin sainit...@gmail.com wrote:
Hi gontchar,
I have done docking analysis using autodock using that ligand and binding
site but i want to do molecular dynamics (MD) using gromacs of same ligand
and binding site of my protein. Thats why i want to know how to place
ligand in specific
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
it is more specific
than Re: Contents of gmx-users digest...
Today's Topics:
1. Re: ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION (Justin A. Lemkul)
2. RMSD (shahid nayeem)
3. Problem during GROMACS 4.5.5 installation (sai nitin)
4. Re: Problem during GROMACS 4.5.5 installation (Justin
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
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
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