Re: AMBER: mm-pbsa

From: vorasit vongsutilers <>
Date: Sun, 19 Mar 2006 09:45:15 -0800 (PST)

Hi Scott,
  Yes, I stripped water from top file, and No, manually using ambpdb on snapshot file also didn't work. For the last question, If you mean the pdb that I used to make unsolvated topology file, it work just fine on rasmol, moilview and xleap. Does vmd tell any difference from those program ?
  Best regard

Scott Pendley <> wrote:

Just to ask the requisite questions before delving too far into problem solving.
1. Since we know that your trajectory file does not have waters or ions, does the parmtop file similarly not have waters or ions?
2. If so, have you tried manually to use ambpdb to create a pdb using unsolvated crd files created in mm_pbsa and the parmtop without solvent/ions?
3. Have you tried to visualize that pdb with a program like vmd, spdbviewer, etc? If so, does it look alright?

Good luck,


  On 3/17/06, vorasit vongsutilers <> wrote: Dr.Gohlke,
  Yes, they contain the same number of atom. Thank you.

Holger Gohlke <> wrote:

    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


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Received on Sun Mar 26 2006 - 06:10:06 PST
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