Hello!!
I am generating a topology file and coordinate file from a PDB structure using xleap. As I load the corresponding topology file and coordinate file to VMD to visualize, it shows that the first residue (a GLU residue) of the protein is having few very large bonds extended in space (these bonds are obviosuly wrong bonds). I did not put the N terminal residue (GLU) as NGLU and C terminal residue (a PRO) as CPRO (I should have done it as per manual) because whenever I put NGLU and CPRO in the pdb, a message appears during the loading in xleap that these residues are not in residue template.
How to resolve this?
regards
Sindrila
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Received on Tue May 24 2011 - 23:00:02 PDT
