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

From: Catein Catherine <askamber23.hotmail.com>
Date: Mon, 21 Jun 2010 14:32:52 +0800

Dear Amber Users and Experts,


I have done xleap analysis and tried to generate prmtop file from a pdb file.


In the pdb file, I named the terminal DNA bases as DA, with PO2 using the atom name of P and O1P and O2P.


Although the pdb file contains PO2, however, whenever I run "a = loadpdb DNA.pdb". The window said P, O1P and O2P is added to the file.


When I type edit a, I found the orginal PO2 is shown as a spot, no bond was connected. I seems to me that ptraj cannot recongize the P, O1P and O2P atoms in the pdb file.


I wonder if it is a wrong naming system.


I tried to open the files with Ambertools 1.2 and 1.4. Both show same error message. However, when I do the same procedures with AMBER 8, the program seems to recongize the PO2, and no new atom was added.


I also tried to source the additional force fields as suggested by Jason. However, I have no luck to get the program works in AmberTools 1.2 or 1.4. I have already patch all bugfix.all for both AmberTools 1.2 and 1.4 already.


Is it a bug in the program or I have miss understand anything here. Could you mind to instruct what's wrong with the naming system?


Best regards,


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Received on Mon Jun 21 2010 - 00:00:03 PDT
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