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