AMBER Archive (2006)

Subject: AMBER: mm-pbsa

From: vorasit vongsutilers (vvorasit_at_yahoo.com)
Date: Thu Mar 16 2006 - 09:34:33 CST

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 ../test.top < ../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

                
---------------------------------
 Yahoo! Mail
 Use Photomail to share photos without annoying attachments.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu