AMBER: how to combine two molecules

From: Wenyong Tong <wenyong_tong.yahoo.com>
Date: Wed, 8 Aug 2007 22:34:33 -0700 (PDT)

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 ____________________________________________________________________________________ Looking for a deal? Find great prices on flights and hotels with Yahoo! FareChase. http://farechase.yahoo.com/
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Received on Sun Aug 12 2007 - 06:07:25 PDT
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