[AMBER] xleap problem for terminal DNA base pairs.

From: Catein Catherine <askamber23.hotmail.com>
Date: Sun, 20 Jun 2010 23:56:59 +0800

Dear Amber users,


I have compiled ambertool 1.2 and amber10 on ubunta 10.1.


I used a pdb file with a DNA strand with 22-base pairs. Using following commands


$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB


However, I found all the terminal residues's PO2 atoms cannot be recongized by the program. I double checked the name of the atoms in my pdb file. For example the first base pairs is named as DA, where the PO2 atom name are as follows P and O1P and O2P. They should be recongizable in xleap. Similarly, I found the residue A in the middle of the DNA are using the same names, and able to be recongized by xleap.


Could you mind to help if I have used the wrong naming system for terminal residues?


Best regards,



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Received on Sun Jun 20 2010 - 09:00:05 PDT
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