AMBER: mm-pbsa

From: vorasit vongsutilers <>
Date: Thu, 16 Mar 2006 07:34:33 -0800 (PST)

Dear Amber user,
  I'm trying to use mm-pbsa to calculate free energy of my modified oligonucleotides and so far I have no luck using this program. The problem happenned when it's try to make pdb by ambpdb. The following is the procedure that I used to make trajectory and topology files.
  Trajectory file
  - Strip water and ions by using ptraj. The original trajectory file is from molecular dynamic run by sander.
  Topology file
  - Make pdb by using ambpdb (topology file is the one that use in molecular dynamic + restart file that created from exact same molecular dynamic). At this step ambpdb worked fine.
  - Delete water and ions residues by using text editor. Save a new pdb without water/ions.
  - Load the pdb in xleap then save topology and coordinate files. (I tried using ambpdb to make pdb from these new file, it crashed down.)
  I placed trajectory and topology file in mm_pbsa tutorial folder. It can generate snapshots but when I started calculation, program stop and left the message.
  "/usr/local/amber8/exe/ambpdb -p ../ < ../01_GenerateSnapshots/test_rec.crd1 > tmp.pdb 2> /dev/null not succesfull"
  I'm sure that I put the right path for the files. I think something might wrong with my topology or/and snapshot files but really couldn't figure it out. Any suggestion would be appreciated. Thank you very much.
  Note - all process performed in Amber 8
  Vorasit Vongsutilers
  Graduate student
  Basic pharmaceutical science
  School of pharmacy, WVU

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Received on Sun Mar 19 2006 - 06:10:21 PST
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