Re: [AMBER-Developers] A Parameter File Editor (that DOESN'T pipe everything through leap);

From: Daniel Roe <>
Date: Wed, 16 Nov 2011 12:42:07 -0500


On Sun, Oct 2, 2011 at 1:18 PM, case <> wrote:
> Sounds great! Can you ask it to strip certain residues, then output the
> corresponding prmtop? Of can ptraj/cpptraj now do this? [I need a "real"
> prmtop, not just for visualization.]

Cpptraj (v2.3.3b) now has the ability to strip and write "real"
prmtops. I've tested cpptraj-stripped topologies against the
equivalent tleap-generated topology using 500-1000 steps of MD and
restarts, trajectories, and energies all match.

Here is a typical command sequence that will strip a topology of all
water/box info and write it out:

parm tz2.parm7
parmstrip :WAT
parmbox nobox
parmwrite tz2.nowat.parm7

Note in this case there is no need to process a trajectory; the parm
can be modified directly. The strip command can still write out the
stripped prmtop, only now it can be used for MD:

parm tz2.parm7
strip :WAT outprefix nowat nobox
trajout netcdf
trajout tz2.nowat.rst7 restart onlyframes 1

This will generate nowat.tz2.parm7 which is the complete parm stripped
of water and box info, which is the stripped netcdf
trajectory, and tz2.nowat.rst7 which is a stripped restart of only
frame 1.

Some details: currently all information in the input parm is modified
except the indexed arrays (nonbond, bond/angle/dihedral
constants/values, SCEE/SCNB). Although the bond/angle/dihedral arrays
are updated the indices are not changed, so there is no need to change
indexed arrays, although this may be added at a future date. There is
no downside to this except there may be some extra information
leftover in the parmtop. Box information is not changed by default,
but can be changed/removed if indicated by the user. The excluded
atoms list is regenerated based on the new bond information, and the
solvent information is generated based on the remaining molecules.
Currently molecule information is not changed; atoms that were
previously in the same molecule will stay that way, even if the bonds
between them are gone. This behavior could easily be changed.

Note that although you can write out an amber topology when reading in
other kinds of files like PDB or mol2, the resulting top will of
course be incomplete and not suitable for MD (although they will still
work for visualization).


Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ   08854
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Received on Wed Nov 16 2011 - 10:00:04 PST
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