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

From: Eric Lang <eric.lang.pg.canterbury.ac.nz>
Date: Wed, 17 Sep 2014 14:48:04 +0000

Hi Jason,

Thanks a lot for your support.

No I used -param to pass the parameter file.

The files I provided last time are for the ligand (which doesn't work with Chamber but with Parmed).

Here I have attached the fragment of concern for my protein (PDB, PSF, as well as the topology and parameter files). Even for this fragment, I have the CMAP problem with Parmed but I can generate the files with Chamber.

Many thanks,

Eric


________________________________
From: Jason Swails <jason.swails.gmail.com<mailto:jason.swails.gmail.com>>
Date: 17 September 2014 15:31
Subject: Re: [AMBER] CHAMBER: problem with water and swissparam generated ligand
To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>


On Wed, Sep 17, 2014 at 8:19 AM, Eric Lang <eric.lang.pg.canterbury.ac.nz<mailto:eric.lang.pg.canterbury.ac.nz>>
wrote:

> 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?
>

​Is this parameter defined in a parameter file that you maybe passed as a
stream file? ParmEd may be a little more picky about what it recognizes as
a "stream" file than chamber.

I will try to reproduce this problem with the files you provided previously.

Thanks!
Jason

--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 17 2014 - 08:00:03 PDT
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