[gmx-users] Problem with pdb2gmx and a new residue

Mark Abraham mark.abraham at anu.edu.au
Mon Sep 20 23:54:35 CEST 2010 

  ----- Original Message ----- From: "Justin A. Lemkul" <jalemkul at vt.edu> Date: Tuesday, September 21, 2010 6:30 Subject: [gmx-users] Problem with pdb2gmx and a new residue To: Gromacs Users' List <gmx-users at gromacs.org>  >  > Hi All, >  > I'm trying to build a topology for a chromophore-containing  > protein using Gromacs 4.5 and OPLS-AA.  The chromophore is  > incorporated into the protein's backbone and the parameters all  > come from a reputable publication, so I've done the following: >  > 1. Created a new .rtp entry > 2. Created an .hdb entry > 3. Defined all nonbonded parameters for new atomtypes in the  > .atp and ffnonbonded.itp file > 4. Defined all new bonded parameters in ffbonded.itp  I think you need to define CRO as Protein in residuetypes.dat so that the pdb2gmx mechanism can deduce that it should form a C-terminal peptide link in the absence of an end-of-chain marker.  Similarly, I have a modified peptide in what's become my "system for generating pdb2gmx bugzilla reports", and with 4.5.1 and git head, if I omit the residuetypes.dat definition I see  Identified residue ALA1 as a starting terminus. Warning: Residue KCX193 in chain has different type (Other) from starting residue ALA1 (Protein). Warning: Residue ASP194 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue ASP195 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue GLU196 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue ASN197 in chain has different type (Protein) from starting residue ALA1 (Protein). More than 5 unidentified residues at end of chain - disabling further warnings. Identified residue THR192 as a ending terminus. <snip> ------------------------------------------------------- Program pdb2gmx_master, VERSION 4.5.1-20100916-6d51340 Source code file: ../../../src/kernel/pdb2gmx.c, line: 655  Fatal error: Atom OXT in residue VAL 467 was not found in rtp entry VAL with 16 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -------------------------------------------------------  This is a bit different, inasmuch as I see the error on the final residue of the first chain, rather then on the modified residue, as you do. However pdb2gmx should cope better with this case - clearly it's confused in the above messages about non-matching types.  We should probably file a bugzilla, even if this fixes your symptoms.  Mark   > The coordinate file was then input into pdb2gmx with an  > oplsaa.ff directory in the working directory.  I received  > the following error (identical with version 4.5 and the most  > recent git with release-4-5-patches): >  > pdb2gmx -f struct.pdb > ... > ------------------------------------------------------- > Program pdb2gmx, VERSION 4.5.1-20100920-03d181e > Source code file: pdb2gmx.c, line: 655 >  > Fatal error: > Atom OXT in residue CRO 331 was not found in rtp entry CRO with  > 39 atoms > while sorting atoms. > . > For more information and tips for troubleshooting, please check  > the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- >  > The CRO residue is my chromophore.  I'm wondering why  > pdb2gmx is finding an OXT atom in the following coordinates: >  > ... > ATOM   2528  N   LEU A  > 330     -13.640  10.888 -25.907   > 1.00  0.00 > ATOM   2529  CA  LEU A  > 330     -12.513  11.013 -26.852   > 1.00  0.00 > ATOM   2530  C   LEU A  > 330     -11.281  10.183 -26.416   > 1.00  0.00 > ATOM   2531  O   LEU A  > 330     -10.625   9.588 - > 27.277  1.00  0.00 > ATOM   2532  CB  LEU A  > 330     -12.159  12.493 -27.066   > 1.00  0.00 > ATOM   2533  CG  LEU A  > 330     -13.206  13.415 -27.691   > 1.00  0.00 > ATOM   2534  CD1 LEU A  > 330     -12.913  14.905 -27.393   > 1.00  0.00 > ATOM   2535  CD2 LEU A  > 330     -13.400  13.160 -29.207   > 1.00  0.00 > ATOM   2536  N   CRO A  > 331     -10.669   9.142 - > 25.611  1.00  0.00 > ATOM   2537  CE  CRO A  > 331      -7.407  12.564 - > 27.240  1.00  0.00 > ATOM   2538  SD  CRO A  > 331      -8.035  12.603 - > 25.595  1.00  0.00 > ATOM   2539  CG1 CRO A  > 331      -8.731  10.996 - > 25.519  1.00  0.00 > ATOM   2540  CB1 CRO A  > 331      -9.618  10.846 - > 24.279  1.00  0.00 > ATOM   2541  CA1 CRO A  > 331     -10.227   9.470 - > 24.406  1.00  0.00 > ATOM   2542  C1  CRO A  > 331     -10.304   8.516 - > 23.260  1.00  0.00 > ATOM   2543  N2  CRO A  > 331      -9.873   8.765 - > 21.981  1.00  0.00 > ATOM   2544  OH  CRO A  > 331      -8.594  11.111 - > 15.969  1.00  0.00 > ATOM   2545  CD2 CRO A  > 331      -9.219   9.756 - > 19.205  1.00  0.00 > ATOM   2546  CE2 CRO A  > 331      -8.888  10.677 - > 18.207  1.00  0.00 > ATOM   2547  CZ  CRO A  > 331      -8.898  10.286 - > 16.863  1.00  0.00 > ATOM   2548  CE1 CRO A  > 331      -9.219   8.975 - > 16.518  1.00  0.00 > ATOM   2549  CD1 CRO A  > 331      -9.549   8.056 - > 17.509  1.00  0.00 > ATOM   2550  CG2 CRO A  > 331      -9.557   8.447 - > 18.848  1.00  0.00 > ATOM   2551  CB2 CRO A  > 331      -9.880   7.417 - > 19.857  1.00  0.00 > ATOM   2552  CA2 CRO A  > 331     -10.149   7.645 - > 21.293  1.00  0.00 > ATOM   2553  C2  CRO A  > 331     -10.726   6.753 - > 22.143  1.00  0.00 > ATOM   2554  O2  CRO A  > 331     -11.108   5.574 - > 21.819  1.00  0.00 > ATOM   2555  N3  CRO A  > 331     -10.810   7.255 - > 23.355  1.00  0.00 > ATOM   2556  CA3 CRO A  > 331     -11.435   6.545 - > 24.488  1.00  0.00 > ATOM   2557  C   CRO A  > 331     -10.492   6.111 - > 25.580  1.00  0.00 > ATOM   2558  O   CRO A  > 331     -10.993   5.596 - > 26.570  1.00  0.00 > ATOM   2559  N   VAL A  > 332      -9.265   5.813 - > 25.096  1.00  0.00 > ATOM   2560  CA  VAL A  > 332      -8.235   4.899 - > 25.607  1.00  0.00 > ATOM   2561  C   VAL A  > 332      -7.512   4.308 - > 24.397  1.00  0.00 > ATOM   2562  O   VAL A  > 332      -6.351   4.567 - > 24.155  1.00  0.00 > ATOM   2563  CB  VAL A  > 332      -7.312   5.633 - > 26.627  1.00  0.00 > ATOM   2564  CG1 VAL A  > 332      -8.127   5.980 - > 27.896  1.00  0.00 > ATOM   2565  CG2 VAL A  > 332      -6.687   6.887 - > 26.051  1.00  0.00 > ... >  > Any ideas on what's going on?  I can upload a bugzilla if  > necessary, I just thought I'd report here first since I'm not  > sure if I'm doing something wrong with respect to the many new  > pdb2gmx features. >  > -Justin >  > --  > ======================================== >  > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >  > ======================================== > --  > gmx-users mailing list    gmx-users at gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at  > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the  > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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