Re: [AMBER] Is it a bug in the xleap of AmberTools 1.2 and 1.4.

From: Catein Catherine <>
Date: Wed, 23 Jun 2010 00:40:47 +0800

Dear Prof. David,


Start with the same pdb file, I startup the xleap in amber10 Ambertool1.2 with the following commands in two different computer.


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


In computer 1, I can read in the pdb file without adding new atoms error message appears.


In computer 2, error message was found in the terminal DNA base pairs. e.g. Following errors appears for the first DA.


Created a new atom named: P within residue: .R<RA5 1>

Created a new atom named: O1P within residue: .R<DA5 1>

Created a new atom named: O2P within residue: .R<DA5 1>




I compared the differences between two version of amber10 (same amber10 tar file as used during installation, but computer 1 was installed 1 year ago, computer 2 is installed recently. The bugfix.all file used in this two installation may be different.). In later case, I found $AMBERHOME/dat/leap/parm/frcmod.ff99SB was loaded. However, in the first case, it is not.


Is it the problem due to "frcmod.ff99SB"? what is the commands line should I used to unload frcmod.ff99SB in the second computer to test it out?




In the pdb file that I open with the xleap, I have PO2 attached to the DA1 already. So, it is there. It is not necessary to add additional PO2 in xleap. When I view the structure in xleap. I found the original PO2 was not connected to the other atoms. According to the error message listed above, the 2nd computer seems to assum DA as DA5. However, in the orginal file, the name DA was used.


What can I do if I want to used the PO2 in the original file instead to build the prmtop files?




When I install ambertools 1.2 to computer 2, i found error messsage of "sleap file cannot be found". However, since I did not used sleap. I only used xleap to generate prmtop only. I ignored this error message. The make test for Amber10 and the rest of the ambertool test are passed. Is it the reason why I found error above?


Best regards,





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Received on Tue Jun 22 2010 - 10:00:03 PDT
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