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