AMBER Archive (2006)

Subject: Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent

From: Petr Kulhanek (kulhanek_at_chemi.muni.cz)
Date: Fri Jul 14 2006 - 04:24:26 CDT

If your topology file contains perturbation information, tool is able to
process only unperturbed part. This means that final topology will not
contain pert. info anymore (but this was never tested).

With regards,
        Petr

j j wrote:
> Thank you,
> If possible I'll be very pleased trying to use this new tool.
> > This tool is able to load topology in AMBER6/7 format and save it in
> > both formats too (6->7 way does not initialize screen and radii
> > sections). Cut part is selected by mask, which has very similar syntax
> > as is used in ptraj.
> Makes this reference about using topology Amber6 gibbs free energy
> perturbations?
> > (especially when you plan to use created topologies for energy
> > calculations).
> Thank you very much,
> JJ
>
>
> 2006/7/14, Petr Kulhanek <kulhanek_at_chemi.muni.cz
> <mailto:kulhanek_at_chemi.muni.cz>>:
>
> Hello,
>
> we have a tool (written in C/C++), which is able to cut any part from
> topology and save it as new one.
>
> This tool is able to load topology in AMBER6/7 format and save it in
> both formats too (6->7 way does not initialize screen and radii
> sections). Cut part is selected by mask, which has very similar syntax
> as is used in ptraj.
>
> If you are interested let me know. But please note that it is still
> experimental thing, which requires prior testing for your case
> (especially when you plan to use created topologies for energy
> calculations).
>
> With regards,
> Petr
>
> j j wrote:
> > Sorry, where I said 'where' I wanted to say 'when'
> >
> > I would like to ask if there is anyway to get new topology file
> > where solvent (or masked residues or atoms from ptraj stripped )
> > from previous one which had included all these residues.
> > The purpose of this questions is about ptraj use, where I'm getting
> > average structures for masked residues stripping the rest.
> > The output I want is a restart file and also a pdb.
> > What I'm doing by now is loading the new pdb into leap, and then
> > another new topology file, but this new just have essential solute
> > information. In this way I need the parm data file, when all
> > was contained in the previous 'big' topology file.
> > Summing up :
> > Is there anyway to delete information from a 'big' topology file
> to get
> > a new one which correspond to the
> > coord files obtained in the same flow of ptraj, or , not by using
> leap &
> > parm files?
> > Thank you very much,
> > JJ
>
> --
> ##################################################
> Petr Kulhanek
> ------------------------------------------------
> E-mail: kulhanek_at_chemi.muni.cz <mailto:kulhanek_at_chemi.muni.cz>
> Phone: +420 - 549 495 459
> WWW: http://www.ncbr.chemi.muni.cz/~kulhanek
> ------------------------------------------------
> National Centre for Biomolecular Research
> Masaryk University
> Kotlarska 2, CZ-611 37 Brno
> Czech Republic
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> 

-- 
##################################################
   Petr Kulhanek
  ------------------------------------------------
   E-mail: kulhanek_at_chemi.muni.cz
   Phone: +420 - 549 495 459
   WWW: http://www.ncbr.chemi.muni.cz/~kulhanek
  ------------------------------------------------
   National Centre for Biomolecular Research
   Masaryk University
   Kotlarska 2, CZ-611 37 Brno
   Czech Republic
##################################################
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