- I am giving commands for complex formation "COM = combine {complex PYR} savepdb COM 1ua7_noh.com.pdb " of protein and ligand while checking its pdb in Discovery studio I checked that the ligand is outside the protein in the solvation box. Is this right or it should be inside the protein after giving the complex formation commands. I am attaching the pdb.
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
Respected Madam
I am working o Amber software not on gromacs.
Please specify the instructions related to Amber.
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