AMBER Archive (2007)

Subject: AMBER: how to combine two molecules

From: Wenyong Tong (wenyong_tong_at_yahoo.com)
Date: Thu Aug 09 2007 - 00:34:33 CDT

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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