----- Original Message ----- From: "Justin A. Lemkul" <jalem...@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@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@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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