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

Justin A. Lemkul jalemkul at vt.edu
Sat Jul 5 02:07:51 CEST 2008


There are a few nomenclature issues with the ffcharmm files.  Rename CD1 
to CD and things should work fine, as far as ILE is concerned.  I 
recalled the .tdb files needing some work as well to meet the format 
requirements.

-Justin

Volker Wirth wrote:
> 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
>
>   

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================




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