AMBER Archive (2006)

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

From: j j (
Date: Thu Jul 13 2006 - 12:59:00 CDT

Thank you very much.
I should have said instead of atoms, counterions,
since also are residues I just strip residues, not
atoms belonging to any residue.
I'll check out rdparm documentation.
Is there any way to transform new style prmtop
into old style prmtop without using leap 6 or oldder?
This should be very usefull for me, since some
old anal/carnal scripts which works with amber6
could be used then.

2006/7/13, Thomas Cheatham <>:
> > 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.
> It is not exactly clear what you want here, but the general answer at
> present is "no". If I understand correctly, you would like to be able to
> use the ptraj strip commands to strip arbitrary atom selections and then
> write out a new prmtop that corresponds to the new (strip'ed) system.
> In general, this is not a trivial problem since as atoms are removed, the
> remaining atoms no longer represent the complete residue and the remaining
> parameters may not meaningfully describe the (partial) residues.
> Decisions have to be made about what the parameters should be. The
> perhaps simplest implementation could be to assume that if an atom is
> deleted, all internal parameters including this atom are removed (i.e. any
> bond, angle, dihedral containing that atom is deleted). This could lead
> to funny topologies (for example if the WAT_at_O atoms of TIP3P waters are
> deleted, you will have a bunch of free hydrogens with no vdw floating
> around) but would solve the problem of LEaP not recognizing the (modified)
> residue from a strip'ed PDB file.
> The only prmtop modification that is currently done in ptraj is changing
> the number of solvent molecules and the resulting prmtop (which must be
> written out) is currently written in old-style prmtop format. rdparm can
> delete specific bonds, angles or dihedrals, however this also outputs the
> old-style prmtop format and the commands are tedious. Given this, at
> present you are stuck with LEaP or must make extensive modifications to
> ptraj.
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