Dear Sir
"Open your com_solvated.pdb file. Identify the mask which denote the ligand.
Suppose residue mask is 556 and if you open the minimized pdb you can
identify some crucial residues such as X1, X2 take out their atom mask.
In the print residue put like this "556,X1,X2"
Say for example you ligand mask is 905 and your crucial amino acid residues
are 902 and 903. Then in print residue put like this "905,902,903"
Thats it."
As per your suggestion to go through com_solvated.pdb file , I have not
generated com_solvted.pdb file. Moreover in the totutorial its saying to
select residue from comlex.prmtop file.
I did go through the complex.pdb file but I am not getting which residue to
slect.
Kindly guide me as to how to go ahead with residue selection.
Thanks
Arunima
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Received on Tue May 27 2014 - 22:30:02 PDT
