Peter -
I can't remember if you sent this to the whole list or not (I only have
one sent to me, but if you send it to both places, I get two coppies, and
I often delete one of those), so I appologize in advance if you only sent
it to me.
On Mon, 22 Nov 2004, Peter Haebel wrote:
On Monday 22 November 2004 20:29, you wrote:
Hi,
I've heard this from a few people, and the answer seems to be that the new
version of APBS doesn't like chain information in the PyMOL-generated PQR
files. I'll release a new version of the plugin that fixes this soon, but
in the meantime, the easy solution is to remove the chain information from
the PDB file before you start the APBS calculation.
how does apbs handle oligomeric proteins if it does not support chain ids? i
think pymol is not happy, if you have residues with identical chain (or no
chain) and identical resi.
- apbs just cares about points in space with radii and charge. in fact,
some of the test cases that come with apbs actually have duplicate residue
ids.
- i think apbs probably supports chain ids pretty well; i think there's
just a mismatch in file formats between pymol-generated pqr files and the
latest apbs.
- i think (this one i haven't tried, but i'm pretty sure) that if you
load the protein up in pymol and then remove the chain ids, pymol will be
just fine.
- PyMOL couldn't assign charges/radii to some of your atoms. Do you have
a non-standard protein residue? If not, it may be that you have a
terminal residue that PyMOL/champ doesn't understand. Can you look at the
PQR file to see which residues ended up with radii and charges of 0?
i have simply attached the original pdb file after refinement with CNS and the
converted pqr file.
there seem to be two problems with
a) C-terminus OT1 and OT2
b) Ser, Thr, Try OH-groups
this is by the way not the original pdb file 1ini, which i only used to
verify
whether or not original pdb files work.
i think the OH groups are fine. those have non-zero radii, so i think
it's just that the standard set of parameters don't put a charge on the
hydrogen there. the terminal THRs, though, are trouble. i think this is
a question for warren:
can champ handle terminal THRs?
(i'm really busy right now, so i don't quite have time to check .. if you
don't get an answer from warren soon, though, i'll double-check).
the first two and last two residues of the chain look like this in the pqr
file:
ATOM 1 N LEU A 6 26.067 12.507 58.949 0.101 1.824
ATOM 2 CA LEU A 6 25.986 11.536 57.819 0.010 1.908
ATOM 3 C LEU A 6 25.209 10.280 58.196 0.612 1.908
ATOM 4 O LEU A 6 24.704 9.579 57.322 -0.571 1.661
ATOM 5 CB LEU A 6 27.394 11.138 57.356 -0.024 1.908
ATOM 6 CG LEU A 6 28.271 12.223 56.726 0.342 1.908
ATOM 7 CD1 LEU A 6 29.621 11.630 56.341 -0.411 1.908
ATOM 8 CD2 LEU A 6 27.578 12.796 55.501 -0.410 1.908
ATOM 9 HD23 LEU A 6 27.308 11.986 54.823 0.098 1.487
ATOM 10 H3 LEU A 6 26.642 12.122 59.684 0.215 0.600
ATOM 11 HA LEU A 6 25.454 12.034 57.009 0.105 1.100
ATOM 12 HB2 LEU A 6 27.282 10.342 56.620 0.026 1.487
ATOM 13 HG LEU A 6 28.430 13.025 57.446 -0.038 1.487
ATOM 14 HD13 LEU A 6 29.914 12.001 55.359 0.098 1.487
ATOM 15 HD22 LEU A 6 28.250 13.487 54.993 0.098 1.487
ATOM 16 H2 LEU A 6 25.140 12.687 59.306 0.215 0.600
ATOM 17 HB3 LEU A 6 27.916 10.861 58.272 0.026 1.487
ATOM 18 HD12 LEU A 6 29.546 10.543 56.312 0.098 1.487
ATOM 19 HD21 LEU A 6 26.677 13.327 55.809 0.098 1.487
ATOM 20 H1 LEU A 6 26.475 13.371 58.621 0.215 0.600
ATOM 21 HD11 LEU A 6 30.369 11.923 57.078 0.098 1.487
ATOM 22 N ASP A 7 25.123 9.988 59.492 -0.516 1.824
ATOM 23 CA ASP A 7 24.402 8.804 59.946 0.038 1.908
ATOM 24 C ASP A 7 22.955 8.814 59.477 0.537 1.908
ATOM 25 O ASP A 7 22.238 9.804 59.631 -0.582 1.661
ATOM 26 CB ASP A 7 24.450 8.684 61.470 -0.030 1.908
ATOM 27 CG ASP A 7 25.795 8.193 61.972 0.799 1.908
ATOM 28 OD1 ASP A 7 26.303 7.191 61.420 -0.801 1.661
ATOM 29 OD2 ASP A 7 26.339 8.801 62.917 -0.801 1.661
ATOM 30 HB2 ASP A 7 23.679 7.983 61.791 -0.012 1.487
ATOM 31 H ASP A 7 25.563 10.594 60.170 0.294 0.600
ATOM 32 HA ASP A 7 24.899 7.940 59.506 0.088 1.387
ATOM 33 HB3 ASP A 7 24.284 9.678 61.886 -0.012 1.487
ATOM 3218 N LEU A 227 17.723 -10.762 41.310 -0.416 1.824
ATOM 3219 CA LEU A 227 18.730 -10.979 42.344 -0.052 1.908
ATOM 3220 C LEU A 227 19.890 -11.839 41.842 0.597 1.908
ATOM 3221 O LEU A 227 21.057 -11.531 42.098 -0.568 1.661
ATOM 3222 CB LEU A 227 18.088 -11.633 43.573 -0.110 1.908
ATOM 3223 CG LEU A 227 17.174 -10.734 44.413 0.353 1.908
ATOM 3224 CD1 LEU A 227 16.527 -11.535 45.530 -0.412 1.908
ATOM 3225 CD2 LEU A 227 17.993 -9.584 44.989 -0.412 1.908
ATOM 3226 HD23 LEU A 227 18.234 -9.795 46.031 0.100 1.487
ATOM 3227 H LEU A 227 16.782 -11.097 41.457 0.272 0.600
ATOM 3228 HA LEU A 227 19.136 -10.005 42.617 0.092 1.387
ATOM 3229 HB2 LEU A 227 18.890 -11.990 44.219 0.046 1.487
ATOM 3230 HG LEU A 227 16.382 -10.332 43.781 -0.036 1.487
ATOM 3231 HD13 LEU A 227 16.466 -10.922 46.429 0.100 1.487
ATOM 3232 HD22 LEU A 227 17.417 -8.661 44.928 0.100 1.487
ATOM 3233 HB3 LEU A 227 17.445 -12.422 43.183 0.046 1.487
ATOM 3234 HD12 LEU A 227 17.125 -12.423 45.734 0.100 1.487
ATOM 3235 HD21 LEU A 227 18.915 -9.474 44.419 0.100 1.487
ATOM 3236 HD11 LEU A 227 15.524 -11.835 45.227 0.100 1.487
ATOM 3237 N THR A 228 19.569 -12.911 41.124 0.000 0.000
ATOM 3238 C THR A 228 20.590 -13.807 40.593 0.000 0.000
ATOM 3239 C THR A 228 21.444 -13.108 39.535 0.000 0.000
ATOM 3240 C THR A 228 19.948 -15.058 39.957 0.000 0.000
ATOM 3241 C THR A 228 21.031 -16.038 39.496 0.000 0.000
ATOM 3242 O THR A 228 19.102 -15.703 40.918 0.000 0.000
ATOM 3243 O THR A 228 20.959 -12.123 38.939 0.000 0.000
ATOM 3244 O THR A 228 22.581 -13.566 39.299 0.000 0.000
ATOM 3245 H THR A 228 22.852 -13.310 38.414 0.000 0.000
ATOM 3246 H THR A 228 18.596 -13.109 40.942 0.000 0.000
ATOM 3247 H THR A 228 21.221 -14.102 41.431 0.000 0.000
ATOM 3248 H THR A 228 22.133 -12.425 39.039 0.000 0.000
ATOM 3249 H THR A 228 19.359 -14.749 39.093 0.000 0.000
ATOM 3250 H THR A 228 21.259 -15.860 38.445 0.000 0.000
ATOM 3251 H THR A 228 18.974 -15.123 41.673 0.000 0.000
ATOM 3252 H THR A 228 20.771 -12.360 38.028 0.000 0.000
ATOM 3253 H THR A 228 20.675 -17.060 39.623 0.000 0.000
ATOM 3254 H THR A 228 21.931 -15.891 40.093 0.000 0.000
TER 3255 THR A 228
-michael
thanks,
-michael
--
This isn't a democracy;| _ |Michael Lerner
it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan
-Torrence, Bring It On| - against HTML email X | Biophysics
| / \ | mler...@umich
On Mon, 22 Nov 2004, Peter Haebel wrote:
Hi Michael,
i have just updated to the latest version of apbs-0.3.2 and pymol-0.97
under debian linux and get the following error messages (see below) + a
completely positively charged protein surface...
using a pqr-file generated at 'http://nbcr.sdsc.edu/pdb2pqr/index.html'
of the same protein works, so there seems to be a problem with the
build-in generation of pqr-files.
i tried 3 different proteins from the PDB with and w/o ligand and water
atoms.
any idea what's going wrong?
cheers,
Peter
-------------------------------------------------------------------------
-----
PDB code 1ini
all waters and ligand atoms removed by hand
...
radiobutton said to generate it Use PyMOL generated PQR and PyMOL
generated Hydrogens and termini so i am returning pymol-generated.pqr
radiobutton said to generate it Use PyMOL generated PQR and PyMOL
generated Hydrogens and termini so i am returning pymol-generated.pqr
WARNING: 5 atoms did not have formal charges assigned
WARNING: 10 atoms did not have properties assigned
...
This executable compiled on Nov 22 2004 at 15:59:46
Parsing input file pymol-generated.in...
parsePBE: Warning -- parsed deprecated "bcfl 1" statement
parsePBE: Please use "bcfl sdh" instead.
NOsh: Warning -- parsed deprecated statment "chgm 1".
NOsh: Please use "chgm spl2" instead!
parsePBE: Warning -- parsed deprecated "srfm 1" statement.
parsePBE: Please use "srfm smol" instead.
parsePBE: Warning -- parsed deprecated "calcenergy 0" statement.
parsePBE: Please use "calcenergy no" instead.
parsePBE: Warning -- parsed deprecated "calcforce 0" statement.
parsePBE: Please use "calcforce no" instead.
Parsed input file.
Got PQR paths for 1 molecules
Reading PQR-format atom data from pymol-generated.pqr.
Valist_readPDB: Unable to parse resSeq token (A) as int!
Valist_readPDB: Error while parsing residue name!
Valist_readPQR: Error parsing ATOM field!
Error while reading molecule from pymol-generated.pqr
Error reading molecules!
ObjectMapLoadDXFile: Loading from 'pymol-generated.dx'.
DXStrToMap: Dimensions: 129 129 97
DXStrToMap: Origin 14.554 -48.010 -7.484
DXStrToMap: Grid 0.579 0.523 0.664
DXStrToMap: 1614177 data points.
ObjectMap: Map Read. Range = 3352.843994 to 12333.959961
___________________________________________
Peter Haebel
Philipps-Universit?t Marburg
Institut f?r Pharmazeutische Chemie
Marbacher Weg 6
D-35032 Marburg
phone: +49-6421-28-25072
fax: +49-6421-28-28994
email: peter.hae...@staff.uni-marburg.de
http://www.agklebe.de
NAD3-Workshop 2005 - Divide&Conquer
http://www.agklebe.de/workshop2005
--
___________________________________________
Dr. Peter Haebel
Philipps-Universit?t Marburg
Institut f?r Pharmazeutische Chemie
Marbacher Weg 6
D-35032 Marburg
phone: +49-6421-28-25072
fax: +49-6421-28-28994
email: peter.hae...@staff.uni-marburg.de
http://www.agklebe.de
NAD3-Workshop 2005 - Divide&Conquer
http://www.agklebe.de/workshop2005
