Should the ligand be inside the protein after the complex combine command in amber provided that ligand was not in real protein PDBID?

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Mansi ..

no, the complex.pdb attached by you is not correct as the distance between both ligand and protein is very large. you have to check the grid dimensions given by you to form the complex.

Amanpreet Kaur

Respected Madam

Thnx for the reply.May I know in which input file should I give the grid dimension and how much to specify so that ligand should be in protein in complex formation

no input is there for specifying the grid dimensions, but if you follow the tutorial available on gromacs official site for protein-ligand complex simulation (link mentioned below), there is mentioned that you have to make 2 different files of ligand and protein from an already made complex that you are using for your simulation.

https://www.bing.com/ck/a?!&&p=46379e97a708a282b24017ce3902b8523e09b149110968fea15c37ad150f092dJmltdHM9MTY1NjU2Njc1MSZpZ3VpZD02ZTJmYTRhZi1lMDg2LTQ3NzMtODc0ZS01YTU4MDYxMGQ4MTEmaW5zaWQ9NTE2Ng&ptn=3&fclid=1b2522e6-f835-11ec-b30a-2cd5af35829a&u=a1aHR0cDovL3d3dy5tZHR1dG9yaWFscy5jb20vZ214L2NvbXBsZXgvaW5kZXguaHRtbA&ntb=1

I am working o Amber software not on gromacs.

Please specify the instructions related to Amber.

I am sorry for that but I can't help you with amber software, I got confused with amber as amber is a type of forcefield that we can use in gromacs software while performing MD simulation