Hello,
Try using AmberTools 1.4 instead of 1.2. If I recall recent responses on
the list correctly, the PDB standard has changed between the releases of
AmberTools 1.4 and AmberTools 1.2. Therefore, you'll probably have better
luck with AmberTools 1.4. Moreover, I think you should be using
leaprc.ff99bsc0 for nucleic acids instead of ff99SB.
Good luck!
Jason
On Sun, Jun 20, 2010 at 11:56 AM, Catein Catherine
<askamber23.hotmail.com>wrote:
>
> 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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Jun 20 2010 - 09:30:03 PDT
