[gmx-users] complex topology file

[Sana Saeed]

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.lady at 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.