Re: [AMBER] CHAMBER: problem with water and swissparam generated ligand

From: Eric Lang <>
Date: Wed, 17 Sep 2014 12:19:58 +0000

Hi Jason,

Thank you so much for improving the error messages for ParmEd. It is indeed a very helpful for troubleshooting.

With this new version of ParmEd, it appears that the problem comes from the CMAP parameters. Here is the error:
        Action chamber failed
           ChamberError: Problem assigning parameters to PSF: No CMAP parameters found for <Cmap; <Atom 1586; 99 ALA [C: C]>-<Atom 1588; 100 GLY [N: NH1]>-<Atom 1590; 100 GLY [CA: CT2]>-<Atom 1593; 100 GLY [C: C]>-<Atom 1595; 101 PRO [N: N]>; cmap_type=None>

So I tried identifying the problem in my files, but I could find anything
there is nothing special about these residues. Here is a PDB extract:
        ATOM 1586 HB3 ALA A 99 25.516 54.144 18.736 0.00 0.00 A H
        ATOM 1587 C ALA A 99 26.370 52.720 16.531 1.00 0.00 A C
        ATOM 1588 O ALA A 99 26.701 52.927 15.376 1.00 0.00 A O
        ATOM 1589 N GLY A 100 25.264 52.076 16.853 1.00 0.00 A N
        ATOM 1590 HN GLY A 100 24.967 51.894 17.790 0.00 0.00 A H
        ATOM 1591 CA GLY A 100 24.393 51.582 15.816 1.00 0.00 A C
        ATOM 1592 HA1 GLY A 100 24.994 51.227 14.990 0.00 0.00 A H
        ATOM 1593 HA2 GLY A 100 23.683 52.353 15.549 0.00 0.00 A H
        ATOM 1594 C GLY A 100 23.622 50.412 16.368 1.00 0.00 A C
        ATOM 1595 O GLY A 100 23.823 50.024 17.525 1.00 0.00 A O
        ATOM 1596 N PRO A 101 22.742 49.811 15.560 1.00 0.00 A N

The parameters for this CMAP are in my parameter file:
        ! glycine before proline map: use glycine map
        C NH1 CT2 C NH1 CT2 C N 24

And the atom numbers corresponding to these 3 residues are in my PSF file:
        1587 1589 1591 1594 1589 1591 1594 1596
(Please note that there is a shift of 1 in the atom numbering given in the error message)

This error do not appear if I use CHAMBER and the prmtop and inpcrd files are generated.

Do you have any idea what the problem could be?

Many thanks in advance,


From: Jason Swails <<>>
Date: 16 September 2014 20:20
Subject: Re: [AMBER] CHAMBER: problem with water and swissparam generated ligand

On Tue, 2014-09-16 at 18:33 +0000, Eric Lang wrote:
> Hi Sarah,
> Thanks a lot for the suggestion.
> Since the -xpsf flag can be used for the XPLOR format, I think it is not anymore required to add that line.
> Nevertheless I gave it a try, but unfortunately it did not work.

Can you try the latest version of ParmEd. The fact that it says "could
not assign parameters" or something means that there is probably
something wrong with your files.

I have hopefully improved the error messages now so that if ParmEd has
this kind of problem again it will spit out what _actually_ went wrong.

Can you try updating ParmEd from the github repository and run it again?
I haven't done anything that will make it "work" (since I suspect
there's some kind of problem with your input or files), but it should
hopefully provide a lot more help hunting down the root cause.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 17 2014 - 05:30:03 PDT
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