please someone help me. i want to find out absolute binding free energy of
protein ligand complex. fisrt i performed docking and selected best poses and
then i made topology file of ligand with PRODRGserver. and then included itp
file of ligand in Protein topology file (from pdb2gmx) , also made complex.gro
as in tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
. can i use these complex files for MD for absolute binding free energy? in
some tutorials the topology file of complex is quite differently organised.
please guide me, i am following decoupling and coupling steps from
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme
Sana Saeed Khan,Teaching-Research AssistantChemoinformatics LabGraduate
Student, MS bioinfoDepartment of BioinformaticsSoongsil University, Seoul,
South Korea.
On Wednesday, February 10, 2016 12:54 AM, Sana Saeed
<bioinformatic.l...@yahoo.com> wrote:
hi gmx usersi want to find out absolute binding free energy of protein ligand
complex. fisrt i performed docking and selected best poses and then i made
topology file of ligand with PRODRGserver. and then included itp file of ligand
in Protein topology file (from pdb2gmx) , also made complex.gro as in tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
. can i use these complex files for MD for absolute binding free energy? in
some tutorials the topology file of complex is quite differently organised.
please guide me, i am following decoupling and coupling steps from
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme
Sana Saeed Khan,Teaching-Research AssistantChemoinformatics LabGraduate
Student, MS bioinfoDepartment of BioinformaticsSoongsil University, Seoul,
South Korea.
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