Re: [AMBER-Developers] [AMBER] Group defining heavy atoms

From: Jason Swails <>
Date: Thu, 22 Jan 2015 10:48:47 -0500

> On Jan 22, 2015, at 9:16 AM, Hannes Loeffler <> wrote:
> On Thu, 22 Jan 2015 08:45:41 -0500
> Jason Swails <> wrote:
>>> On Jan 22, 2015, at 8:33 AM, Gerald Monard
>>> <> wrote:
>>> Hi,
>>> What about reading an external file? It's already the case for
>>> distance restraints for example.
>> But the distance (and all NMR-related) restraints still take input
>> through a namelist, which is subject to the same limitations as I
>> mentioned earlier. And I don’t think we need yet another free-format
>> input spec. [1]
>> I think the solution here is pretty straightforward -- expand the
>> character limit and change restraintmask and restraint_wt into
>> arrays. That way, backwards compatibility is maintained, and we
>> support multiple selection groups through the mask interface. The
>> necessary changes should be small, which is the biggest upside :).
> Somewhat related, and possibly solving problems likes this but only in
> part, would be a feature I always wanted to have for higher flexibility
> in defining masks. What I miss is higher level descriptions of e.g.
> "proteins" or "nucleotides" or "lipids" or "backbone", etc. Could
> probably be simply implemented through additional sections in the
> prmtop file.

Something like VMD’s or PyMol’s selection syntax would indeed be nice. I suspect it will be both time-consuming and somewhat difficult, though (I watched someone implement it in a Python package, but they made extensive use of a high-level library for parsing and interpreting the selection strings, which we wouldn’t have available in Fortran).

> This reminds me, what ever happened to the proposal some years back to
> retain certain information from the PDB like chain IDs and original
> residue numbers in the prmtop?

That was offloaded to a separate program (add_pdb). That functionality is now part of (and expanded by) ParmEd via the “addPDB” command. It adds the RESIDUE_CHAINID, RESIDUE_ICODE, RESIDUE_NUMBER, ATOM_OCCUPANCY, ATOM_BFACTOR, and ATOM_NUMBER sections to the prmtop file by comparing it with a PDB file and filling in the relevant information.

The only programs that currently reads that data in, though, are cpptraj and ParmEd (which is most useful if used through the API, where the extra atom and residue properties are readily available as simple attributes).

> Also, what is the "set ... restype" in
> leap used for?

Not sure. Basic grepping suggests.... nothing.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER-Developers mailing list
Received on Thu Jan 22 2015 - 08:00:03 PST
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