[gmx-users] State B IN Topology

Sana Saeed bioinformatic.lady at yahoo.com
Wed Feb 24 01:32:07 CET 2016

HIi am making topology of protein ligand complex for calculating binding free energy. my question is do i need to define state B manually or is there any automatic method to do that. Second question is i want of number my ligand atom numbers from the number where protein atom numbers are stopped , like if protein's last atom is 100 then i want to start my ligand from 101. manually it will take lots of time because i will have to modify all the sections in topology file, is there any easy method? or i need to do that manually. Thanks in advance Sana Saeed Khan,Teaching-Research AssistantChemoinformatics LabGraduate Student, MS bioinfoDepartment of BioinformaticsSoongsil University, Seoul, South Korea.

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