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 - 02:44:09 CDT

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 

-- 
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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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