[gmx-users] Atom CD in residue ILE 1 not found in rtp entry with 19 atoms

[Volker Wirth]

Hello list,

I tried out the Membrane Builder at www.charmm-gui.org, which
generates CHARMM input files for a combinded membrane-protein system
and it looks quite good. The conversion CHARMM -> GROMACS is a bit
tricky, I know, but I wanted to try it, though:

Using the Perl script on
http://www.gromacs.org/component/option,com_docman/task,doc_details/gid,59/
I converted the CHARMM force field par_all27_prot_lipid.prm (found at
http://mackerell.umaryland.edu/CHARMM_ff_params.html) to a
GROMACS-like .itp file.

I used the files of
http://www.gromacs.org/old/topologies/uploaded_force_fields/charmm_gromacs.tar.gz
(containing amongst others ffcharmm.itp and ffcharmm.rtp),  so -ff
charmm is available in pdb2gmx. (According to the readme file, now it
should be possible to execute pdb2gmx and create a .top file, that has
to be modified further by charmm27-run-addtop-gromacs-dihe.sh, also
included in this tar.gz.)

When I tried to execute
pdb2gmx -ignh -ff charmm -f usedfile.pdb -o usedfile_new.pdb -p
usedfile_new.top -ter
I got some errors first because of the terminal database files
ffcharmm-c.tdb and ffcharmm-n.tdb, which had to be edited (simply
remove some columns, then it works).

But now I can't find out how to handle
"Fatal Error:
Atom CD in residue ILE 1 not found in rtp enrty with 19 atoms
                        while sorting atoms"

Sorry for that long mail, but to make the problem clear, here are
parts cited from the used files:

ffcharmm.rtp
---------------------------------------------------------------------------------------------
[   bondedtypes   ]
;   bonds   angles   dihedrals   impropers   all_dihedrals   nrexcl
1   1   3   1   1   3
.
.
.
[   ILE   ]
[   atoms   ]
N   NH1   -0.470   1
H    H   0.310   1
CA   CT1   0.070   1
HA   HB   0.090   1
CB   CT1   -0.090   2
HB   HA   0.090   2
CG2   CT3   -0.270   3
HG21   HA   0.090   3
HG22   HA   0.090   3
HG23   HA   0.090   3
CG1   CT2   -0.180   4
HG11   HA   0.090   4
HG12   HA   0.090   4
CD1   CT3   -0.270   5
HD11   HA   0.090   5
HD12   HA   0.090   5
HD13   HA   0.090   5
C   C   0.510   6
O   O   -0.510   6
[   bonds   ]
CB   CA
CG1   CB
CG2   CB
CD1   CG1
N   H
N   CA
C   CA
C   +N
CA   HA
CB   HB
CG1   HG11
CG1   HG12
CG2   HG21
CG2   HG22
CG2   HG23
CD1   HD11
CD1   HD12
CD1   HD13
O   C
[   impropers   ]
N   -C   CA   H    improper_NH1_X_X_H_
C   CA   +N   O   improper_O_X_X_C_
.
.
.
---------------------------------------------------------------------------------------------

used.pdb
---------------------------------------------------------------------------------------------
REMARK  GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) ON JUL,
04. 2008.
REMARK  ASSEMBLE PREVIOUSLY GENERATED COMPONENTS (LIPID BILAYER,
PROTEIN, PORE WATER,
REMARK   DATE:     7/ 4/ 8      1:54: 9      CREATED BY USER: apache
ATOM      1  N   ILE   046      -5.242 -23.250  10.686  1.00  0.00      PROA
ATOM      2  HT1 ILE   046      -4.310 -23.370  11.132  1.00  0.00      PROA
ATOM      3  HT2 ILE   046      -5.645 -24.184  10.470  1.00  0.00      PROA
ATOM      4  HT3 ILE   046      -5.874 -22.742  11.337  1.00  0.00      PROA
ATOM      5  CA  ILE   046      -5.098 -22.491   9.461  1.00  0.00      PROA
ATOM      6  HA  ILE   046      -4.770 -21.491   9.715  1.00  0.00      PROA
ATOM      7  CB  ILE   046      -4.187 -23.220   8.460  1.00  0.00      PROA
ATOM      8  HB  ILE   046      -4.600 -24.259   8.411  1.00  0.00      PROA
ATOM      9  CG2 ILE   046      -4.198 -22.499   7.121  1.00  0.00      PROA
ATOM     10 HG21 ILE   046      -3.671 -23.099   6.350  1.00  0.00      PROA
ATOM     11 HG22 ILE   046      -5.238 -22.335   6.768  1.00  0.00      PROA
ATOM     12 HG23 ILE   046      -3.694 -21.512   7.197  1.00  0.00      PROA
ATOM     13  CG1 ILE   046      -2.758 -23.330   9.028  1.00  0.00      PROA
ATOM     14 HG11 ILE   046      -2.272 -22.329   9.022  1.00  0.00      PROA
ATOM     15 HG12 ILE   046      -2.817 -23.661  10.090  1.00  0.00      PROA
ATOM     16  CD  ILE   046      -1.847 -24.309   8.292  1.00  0.00      PROA
ATOM     17  HD1 ILE   046      -0.859 -24.371   8.798  1.00  0.00      PROA
ATOM     18  HD2 ILE   046      -2.295 -25.326   8.277  1.00  0.00      PROA
ATOM     19  HD3 ILE   046      -1.677 -23.984   7.244  1.00  0.00      PROA
ATOM     20  C   ILE   046      -6.487 -22.360   8.876  1.00  0.00      PROA
ATOM     21  O   ILE   046      -6.913 -21.277   8.501  1.00  0.00      PROA
ATOM     22  N   LYS   047      -7.199 -23.476   8.826  1.00  0.00      PROA
ATOM     23  HN  LYS   047      -6.862 -24.356   9.156  1.00  0.00      PROA
ATOM     24  CA  LYS   047      -8.547 -23.497   8.277  1.00  0.00      PROA
ATOM     25  HA  LYS   047      -8.620 -22.640   7.618  1.00  0.00      PROA
ATOM     26  CB  LYS   047      -8.783 -24.823   7.551  1.00  0.00      PROA
ATOM     27  HB1 LYS   047      -8.548 -25.639   8.273  1.00  0.00      PROA
ATOM     28  HB2 LYS   047      -9.866 -24.918   7.313  1.00  0.00      PROA
.
.
.
---------------------------------------------------------------------------------------------

OK, the 21 lines in .pdb will hardly fit the 19 lines in .rtp, and the
easiest solution might be to edit the .rtp file, but everything I
tried so far failed, as I'm not too familiar with GROMACS.

Hope you know a possibile solution, thanks in advance!

Enjoy your weekend, best
Volker

-- 
###################################
Volker Wirth
Center for Medical Physics and Technology
Biophysics Group
FAU Erlangen-Nuremberg

Email: vwirth%at%biomed.uni-erlangen.de
###################################