Dear All, I am able to do the superposition of the ligand with suplig.f program and superpose also do the same. Thank you for your valuable suggestions.
regardsvijay Vijay On Tuesday, 26 May 2015 6:11 PM, vijay srivastava <vijaytec...@yahoo.co.in> wrote: Dear All, I want to superpose the nucleotide form one GTPase on to the nucleotide of other GTPase in order to study the interaction in the nucleotide binding pocket. I tried to superpose but it is superposing on the basis of secondary structure as aresult both the nucleotides from two structutres are not properly aligned. I want to superpose both the nucleotide, so that I will get the matrix, which I want to apply on my desired strcuture and study the interacting residues.Do any one have the align program with you or any other program which can solve this problem. waiting for your kind response regardsvijay