[gmx-users] how to set Restraints

Sana Saeed bioinformatic.lady at yahoo.com
Fri Feb 19 03:12:04 CET 2016

 hisir Justin Lemkul  and gmx usersi am stuck in a problem. i am performing MD simulation of complex of protein and ligand for binding free energy calculation. i have done all the basics of MD, performed all the BEVANLAB tutorials for my learning and some other papers examples. but i never dealt with binding free energy calculations , so in different tutorials they have the complex topology, which is my problem, i made ligand and protein topologies but now i dont know how to get distance, dihedral and angle restraints, Sir Justin Lemkul you replied me "To include intermolecular restraints and bonded terms, just use [intermolecular_interactions] at the end of the .top (available in versions 5.1 and newer).  Use global atom numbers to define the interactions." can you a little bit explain how to do that.Thanks in advance
Sana Saeed Khan,Teaching-Research AssistantChemoinformatics LabGraduate Student, MS bioinfoDepartment of BioinformaticsSoongsil University, Seoul, South Korea.

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