[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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