Hi Jason,
Awesome, thanks a lot!
I am glad it helped to fix this bug.
With the new version of Parmed, I can now convert the PSF and PDB files that include my protein and the ligands, which is really great.
However, I have a new problem, but at least this time I have identified the cause:
I am working with a big solvated system and thus I have a very large number of atoms: more than 99,999...
Therefore the atom numbering switches to hexadecimal to conserve the PDB column sizes:
ATOM 99998 H1 TIP3W3580 -31.552 26.681 43.524 1.00 0.00 WT4 H
ATOM 99999 H2 TIP3W3580 -31.867 26.800 44.896 1.00 0.00 WT4 H
ATOM 186a0 OH2 TIP3W3583 -14.658 19.993 51.182 1.00 0.00 WT4 O
ATOM 186a1 H1 TIP3W3583 -15.178 20.681 50.585 1.00 0.00 WT4 H
ATOM 186a2 H2 TIP3W3583 -14.335 19.304 50.572 1.00 0.00 WT4 H
When I try to use Parmed on the PSF/PDB of my whole solvated system, I have the following error:
parmed_commands.cmdloop()
File "/usr/lib/python2.7/cmd.py", line 142, in cmdloop
stop = self.onecmd(line)
File "/usr/lib/python2.7/cmd.py", line 221, in onecmd
return func(arg)
File "<string>", line 1, in <lambda>
File "/usr/local/lib/python2.7/dist-packages/ParmedTools/parmed_cmd.py", line 141, in _normaldo
action.execute()
File "/usr/local/lib/python2.7/dist-packages/ParmedTools/ParmedActions.py", line 3516, in execute
crd = ChemicalSystem.load_from_pdb(self.crdfile)
File "/usr/local/lib/python2.7/dist-packages/chemistry/system.py", line 206, in load_from_pdb
return cls.load_from_open_pdb(open(pdb, 'r'))
File "/usr/local/lib/python2.7/dist-packages/chemistry/system.py", line 262, in load_from_open_pdb
altloc=altloc),
File "/usr/local/lib/python2.7/dist-packages/chemistry/system.py", line 72, in __init__
super(Atom, self).__init__(*args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/chemistry/system.py", line 39, in __init__
self._types[self._ordered_args[i]](arg))
ValueError: invalid literal for int() with base 10: '186a0'
So it seems that Parmed do not recognised the hexadecimal numbering.
I had a quick look at system.py and I saw that you have a test to see if the residue number is hexadecimal, but I don't think I saw something for the atom number. Do you think this can be easily fixed? If not is there any other way to get round of this problem?
By the way regarding the hexadecimal test for the residue number, I had a look at my PDB files, and I saw that VMD (or PSFGEN or SOLVATE, I am not sure which one), do not switch to hexadecimal numbering after 9999 for the residue number, instead it restarts the numbering from 1 but changes the "segname" number (see for example below where the segname change from WAT1 to WAT2).
ATOM 51835 OH2 TIP3W9999 -9.810 2.513 -32.630 1.00 0.00 WAT1 O
ATOM 51836 H1 TIP3W9999 -9.976 2.772 -33.536 1.00 0.00 WAT1 H
ATOM 51837 H2 TIP3W9999 -9.078 3.060 -32.345 1.00 0.00 WAT1 H
ATOM 51838 OH2 TIP3W 1 -13.494 -46.453 -25.565 1.00 0.00 WAT2 O
ATOM 51839 H1 TIP3W 1 -13.825 -46.812 -24.741 1.00 0.00 WAT2 H
ATOM 51840 H2 TIP3W 1 -13.746 -45.531 -25.553 1.00 0.00 WAT2 H
Later in the PDB file, VMD doesn't wait to reach 9999 to start a new segname and do not necessary restart at 1, see for example:
ATOM 1958b OH2 TIP3W9260 0.636 11.509 56.128 1.00 0.00 WT4 O
ATOM 1958c H1 TIP3W9260 1.069 10.681 55.969 1.00 0.00 WT4 H
ATOM 1958d H2 TIP3W9260 0.543 11.679 57.135 1.00 0.00 WT4 H
ATOM 1958e OH2 TIP3W 2 13.925 6.927 -52.530 1.00 0.00 WT5 O
ATOM 1958f H1 TIP3W 2 14.107 6.026 -52.541 1.00 0.00 WT5 H
ATOM 19590 H2 TIP3W 2 13.089 6.988 -52.946 1.00 0.00 WT5 H
ATOM 19591 OH2 TIP3W 3 22.542 -1.590 -54.002 1.00 0.00 WT5 O
ATOM 19592 H1 TIP3W 3 22.312 -1.568 -53.025 1.00 0.00 WT5 H
ATOM 19593 H2 TIP3W 3 21.824 -1.187 -54.404 1.00 0.00 WT5 H
So I was just wondering if this matters or not for the conversion of the PSF-PDB files into INPCRD-PRMTOP files and if so, if Parmed takes this into account?
Last question: I cannot open in VMD the prmtop file generated by Parmed. I have noticed that with Chamber one can add the -vmd flag to generate "vmd-friendly" prmtop files. Does Parmed do the same? If not how can I visualize it?
Many thanks in advance and thank you so much for all your support.
Cheers,
Eric
________________________________
From: Jason Swails <jason.swails.gmail.com<mailto:jason.swails.gmail.com>>
Date: 17 September 2014 19:53
Subject: Re: [AMBER] CHAMBER: problem with water and swissparam generated ligand
To: amber.ambermd.org<mailto:amber.ambermd.org>
On Wed, 2014-09-17 at 12:19 +0000, Eric Lang 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?
I found and fixed the problem. Thanks for the report! The problem was
basically that ParmEd would read all of the CMAP terms, but it would
never actually _add_ the last one to the parameter database.
I have fixed this and it now works for the test case you sent me.
Please update your ParmEd installation and see if it works now.
Thanks again!
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Sep 18 2014 - 03:00:05 PDT
