AMBER Archive (2005)

Subject: AMBER: Loading pdb-residue (re)numbering in leap

From: gtg549i_at_mail.gatech.edu
Date: Tue May 31 2005 - 12:48:13 CDT

Dear amber users,
I noticed that when I load a pdb file of organic molecules (like methacrylic
acid) into xleap the residue numbers (a.k.a sequence numbers) get renumbered
because the xleap didn't recognize the residue (This is as described in the
section 3 of tutorial 1). Is there a way to preserve the original residue
numbering as listed in the PDB? I won't have to map between the biologically
relevant residue numbers to amber's residue numbering. When i use edit
command to look at the molecules, i found that there is missing of bonds.

Secondly, i want to study the binding interaction between two organic
molecules, how can i create the pdb file of the complex? I put the two
molecules in Viewlite and save it and load this file into xleap. The complex
got renumbered again. How i can let xleap recognize my complex?

Attachment are the pdb files of two molecules (BE2 and MAA) and their complex.

Thanks in advance, Shuting

  • application/vnd.palm attachment: BE2.pdb

  • application/vnd.palm attachment: MAA.pdb


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