Hello Amber Users,
I have two pdb files: one is sugar produced by Leap; another is lipid, and I used antechamber to get .prepin and frocmod files.
I wonder how to combine these two molecules. I tried the Leap: "Sequence" command and it seems the distance is a problem. I tried using Insight II to combine them and .mol2 files. When I loaded this file into Leap and check unit, I got the following message:
Checking for bond parameters.
Could not find bond parameter for: O.3 - C.3
Could not find bond parameter for: O.3 - C.3
…….
Checking for angle parameters.
Could not find angle parameter: O.3 - C.3 - O.3
…….
I compared the Prepin and glycam04.prep files with my .mol2 files. There are no differences of atom name among those files.
Anyone can give me some suggestions? Thanks in advance!
Wenyong
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Received on Sun Aug 12 2007 - 06:07:25 PDT
