AMBER Archive (2006)

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

From: j j (fantvamp_at_gmail.com)
Date: Fri Jul 14 2006 - 03:48:33 CDT

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>:
>
> 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
> 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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