AMBER Archive (2006)

Subject: Re: AMBER: mm-pbsa

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Mon Mar 20 2006 - 12:06:38 CST

Do you get any errors from ambpdb when you tried to create the pdb?

Also could you send me directly the two unsolvated files (parmtop and
coordinate)? I might get a better idea from looking at them.

On 3/19/06, vorasit vongsutilers <vvorasit_at_yahoo.com> wrote:
>
> 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
> Vorasit
>
>
>
> *Scott Pendley <scott.pendley_at_gmail.com>* wrote:
>
> Vorasit,
>
> 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,
>
> Scott
>
> On 3/17/06, vorasit vongsutilers <vvorasit_at_yahoo.com> wrote:
> >
> > Dr.Gohlke,
> >
> > Yes, they contain the same number of atom. Thank you.
> >
> > Vorasit
> >
> >
> > *Holger Gohlke <gohlke_at_bioinformatik.uni-frankfurt.de>* 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
> >
> > Holger
> >
> > ------------------------------
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>

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