Re: AMBER: mm-pbsa

From: Holger Gohlke <>
Date: Thu, 16 Mar 2006 18:33:20 +0100

Am Donnerstag, 16. März 2006 16:34 schrieb vorasit vongsutilers:
> 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.)

>From the information you provide everything looks ok to me. However, that you
are not able to generate a pdb file at this step already indicates a problem
(and it is not astonishing that mm_pbsa "further down" also fails). As an
initial check - are the number of atoms in both the topology and coordinate
files you use here the same?

Best regards


> 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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Dr. Holger Gohlke
Juniorprofessur fuer Molekulare Bioinformatik
J.W. Goethe-Universitaet
Fachbereich Biowissenschaften
Institut für Zellbiologie und Neurowissenschaft
Max-von-Laue-Str. 9
60438 Frankfurt/Main
Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29527
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Received on Sun Mar 19 2006 - 06:10:21 PST
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