CCL: How to combine two PDB files

 Sent to CCL by: "Ross Walker" [ross=rosswalker.co.uk]
 Hi Wenyong,
 Amber specific questions are best posted to the amber mailing list. See
 http://amber.scripps.edu
 for details.
 > I have two pdb files: one is sugar produced by Leap;
 > another is lipid, and I used antechamber to get
 > .prepin and frocmod files. Both of them can be loaded
 > in xleap seperately.
 >
 > I wonder how to combine these two PDB files and make a
 > single bond between them.
 Since you likely didn't set any head or tail atoms for these residues you
 can do the following. Take the sugar pdb and add a TER card on the end. The
 cat the lipid pdb file onto the end of the sugar one. You will need to
 renumber the residues to make sure they have unique residue IDs.
 Then open leap. source leaprc.gaff, load the two prepin files. Load the two
 frcmod files, Then load the pdb file. Then either manually (using edit in
 xleap) or using leap's bond command add a bond between the two residues as
 needed. Note you may have to provide a parameter for this bond. If so then
 you will need to add the parameters to one of the frcmod files and repeat
 the above. You will find this out when you try to use saveamberparm.
 All the best
 Ross
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