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,
Cat
_________________________________________________________________
Hotmail: Trusted email with Microsoft¡¦s powerful SPAM protection.
https://signup.live.com/signup.aspx?id=60969
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 21 2010 - 00:00:03 PDT
