Hello!!
I am trying to generate 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 the corresponding structure of protein, it shows that the first residue of the protein is connected with a group (most probable -NH3 group) via a large bond which is far from the protein chain. I want to know why it is looking so and how to rectify it?
Note: I have not mentioned the N-terminal (GLU) and C-terminal amino acid (PRO) as NGLU and CPRO in the pdb. As I am changing the GLU and PRO to NGLU and NPRO it is showing that 17 residues are not in residue template.
I want to know what is the general formate of a PDB which can be used as a input file for xleap. How to modify the PDB files?
Sindrila
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Received on Tue May 24 2011 - 07:30:03 PDT
