Hi, I just added this to the existing .rtp file in gromos
[ LIG ] [ atoms ] C C 0.000 0 F F 0.000 0 [ SCH ] [ atoms ] O OM 0.000 0 C C 0.000 0 O O 0.000 0 F F 0.000 0 S S 0.000 0 H H 0.000 0 I also added LIG and SCH to the residuetypes.dat Kind regards, Ehsan ----- Original Message ----- From: "Justin Lemkul" <jalem...@vt.edu> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Sent: Friday, September 27, 2013 12:29:38 PM Subject: Re: [gmx-users] ionomer topolgy On 9/27/13 3:17 PM, Ehsan Sadeghi wrote: > Many thanks Justin. > > Here is my .pdb file: > > ATOM 1 C LIG 1 -10.450 5.214 -1.717 1.00 0.00 C > ATOM 2 C LIG 1 -8.424 5.477 -1.030 1.00 0.00 C > ATOM 3 C LIG 1 -6.603 5.864 -0.166 1.00 0.00 C > ATOM 4 F LIG 1 -6.651 6.230 -1.691 1.00 0.00 F > ATOM 5 F LIG 1 -8.417 4.546 -2.349 1.00 0.00 F > ATOM 6 C LIG 1 -5.705 3.003 1.204 1.00 0.00 C > ATOM 7 F LIG 1 -7.247 5.032 1.683 1.00 0.00 F > ATOM 8 F LIG 1 -8.521 5.307 0.400 1.00 0.00 F > ATOM 9 C LIG 1 -3.913 4.878 2.109 1.00 0.00 C > ATOM 10 F LIG 1 -4.358 3.650 -0.024 1.00 0.00 F > ATOM 11 F LIG 1 -6.198 1.346 0.214 1.00 0.00 F > ATOM 12 C LIG 1 -1.306 5.673 2.286 1.00 0.00 C > ATOM 13 F LIG 1 -3.429 3.111 0.668 1.00 0.00 F > ATOM 14 F LIG 1 -2.358 3.855 1.570 1.00 0.00 F > ATOM 15 C LIG 1 0.246 3.040 2.048 1.00 0.00 C > ATOM 16 F LIG 1 -0.514 4.358 3.241 1.00 0.00 F > ATOM 17 F LIG 1 -0.928 3.807 1.741 1.00 0.00 F > ATOM 18 C LIG 1 1.925 3.706 2.014 1.00 0.00 C > ATOM 19 F LIG 1 -0.226 2.548 0.094 1.00 0.00 F > ATOM 20 F LIG 1 0.215 1.482 1.590 1.00 0.00 F > ATOM 21 F LIG 1 -11.789 4.355 -2.598 1.00 0.00 F > ATOM 22 F LIG 1 -11.552 4.133 -0.632 1.00 0.00 F > ATOM 23 F LIG 1 2.299 2.385 2.438 1.00 0.00 F > ATOM 24 F LIG 1 1.831 1.994 1.526 1.00 0.00 F > ATOM 25 OM SCH 2 3.334 3.720 1.360 1.00 0.00 O > ATOM 26 C SCH 2 5.273 2.985 0.897 1.00 0.00 C > ATOM 27 C SCH 2 6.100 2.445 1.642 1.00 0.00 C > ATOM 28 F SCH 2 4.528 2.997 1.631 1.00 0.00 F > ATOM 29 F SCH 2 6.122 3.473 0.467 1.00 0.00 F > ATOM 30 C SCH 2 7.274 1.746 2.026 1.00 0.00 C > ATOM 31 OM SCH 2 5.454 2.160 2.446 1.00 0.00 O > ATOM 32 F SCH 2 6.788 2.944 0.993 1.00 0.00 F > ATOM 33 F SCH 2 7.031 1.025 2.779 1.00 0.00 F > ATOM 34 F SCH 2 8.010 2.431 2.393 1.00 0.00 F > ATOM 35 F SCH 2 7.678 1.241 1.173 1.00 0.00 F > ATOM 36 C SCH 2 5.042 1.305 2.243 1.00 0.00 C > ATOM 37 C SCH 2 5.168 0.043 2.583 1.00 0.00 C > ATOM 38 F SCH 2 4.938 1.296 1.178 1.00 0.00 F > ATOM 39 F SCH 2 4.377 1.446 3.070 1.00 0.00 F > ATOM 40 S SCH 2 5.516 -1.463 2.733 1.00 0.00 S > ATOM 41 F SCH 2 4.304 0.015 3.213 1.00 0.00 F > ATOM 42 F SCH 2 6.073 0.088 2.014 1.00 0.00 F > ATOM 43 O SCH 2 4.555 -2.079 3.473 1.00 0.00 O > ATOM 44 H SCH 2 4.772 -3.020 3.567 1.00 0.00 H > ATOM 45 O SCH 2 6.692 -1.508 1.977 1.00 0.00 O > ATOM 46 O SCH 2 6.001 -2.846 2.762 1.00 0.00 O > CONECT 1 2 21 22 > CONECT 2 1 3 4 5 > CONECT 2 > CONECT 3 2 6 7 8 > CONECT 3 > CONECT 4 2 > CONECT 5 2 > CONECT 6 3 9 10 11 > CONECT 6 > CONECT 7 3 > CONECT 8 3 > CONECT 9 6 12 13 14 > CONECT 9 > CONECT 10 6 > CONECT 11 6 > CONECT 12 9 15 16 17 > CONECT 12 > CONECT 13 9 > CONECT 14 9 > CONECT 15 12 18 19 20 > CONECT 15 > CONECT 16 12 > CONECT 17 12 > CONECT 18 15 23 24 25 > CONECT 18 > CONECT 19 15 > CONECT 20 15 > CONECT 21 1 > CONECT 22 1 > CONECT 23 18 > CONECT 24 18 > CONECT 25 18 26 > CONECT 26 25 27 28 29 > CONECT 26 > CONECT 27 26 30 31 32 > CONECT 27 > CONECT 28 26 > CONECT 29 26 > CONECT 30 27 33 34 35 > CONECT 30 > CONECT 31 27 36 > CONECT 32 27 > CONECT 33 30 > CONECT 34 30 > CONECT 35 30 > CONECT 36 31 37 38 39 > CONECT 36 > CONECT 37 36 40 41 42 > CONECT 37 > CONECT 38 36 > CONECT 39 36 > CONECT 40 37 43 45 46 > CONECT 40 > CONECT 41 37 > CONECT 42 37 > CONECT 43 40 44 > CONECT 44 43 > CONECT 45 40 > CONECT 46 40 > MASTER 0 0 0 0 0 0 0 0 46 0 46 0 > END > > ------------------------------------------------- > I already added LIG and SCH in residuetypes.dat and defined the atoms for > each residue in aminoacids.rtp in gromos. When I run pdb2gmx -f nafion.pdb > I receive this error: > > > Warning: Starting residue LIG1 in chain not identified as Protein/RNA/DNA. > Warning: Starting residue SCH2 in chain not identified as Protein/RNA/DNA. > Problem with chain definition, or missing terminal residues. > This chain does not appear to contain a recognized chain molecule. > If this is incorrect, you can edit residuetypes.dat to modify the behavior. > 8 out of 8 lines of specbond.dat converted successfully > > ------------------------------------------------------- > Program pdb2gmx, VERSION 4.6.3 > Source code file: > /home/ehssad/Downloads/Gromacs/gromacs-4.6.3/src/kernel/resall.c, line: 642 > > Fatal error: > Residue 'LIG' not found in residue topology database > For more information and tips for troubleshooting, please check the GROMACS > You still haven't provided any real useful diagnostic information. What do the .rtp entries look like? Which force field did you modify? Did you modify a local copy of it, or the one in $GMXLIB? Based on that, are you making the right choice when running pdb2gmx? -Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- 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? 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