Dear all, I thought that I would reply to this thread as I am having similar problems and there didn't seem to be an obvious solution. I wanted to run a simulation of a POPE bilayer using the Charmm36 parameters from the Gromacs website. So I used pdb2gmx to generate a .top file.
I used the input file from this website: wget http://terpconnect.umd.edu/~jbklauda/research/download/pope80-c36npt.pdb pdb2gmx -f pope80-c36npt.pdb -o pope.pdb -p pope.top -ff charmm36 (I then selected option 3 (tips3p charmm water)) I found that whilst pdb2gmx completes 'successfully', no bond, angle or dihedral terms are generated in the resulting top file. I found this behaviour when running both pdb2gmx version 4.5.3 and version 4.5.4. As a further check I also found the same behaviour if I used the charmm27 parameters. I found this related thread, but there was no obvious solution to the problem. As far as I can tell I am using a reasonable procedure. Can anyone spot something that I'm doing wrong to cause this behaviour? I have pasted the output from pdb2gmx below and truncated results from the top file below this. Many thanks in advance, Jon :-) G R O M A C S (-: GROningen Mixture of Alchemy and Childrens' Stories :-) VERSION 4.5.3 (-: ... ... Using the Charmm36 force field in directory charmm36.ff Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/watermodels.dat Select the Water Model: 1: TIP3P TIP 3-point, recommended 2: TIP4P TIP 4-point 3: TIPS3P CHARMM TIP 3-point with LJ on H's (note: twice as slow in GROMACS) 4: SPC simple point charge 5: SPC/E extended simple point charge 6: None 3 Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/aminoacids.r2b Reading pope80-c36npt.pdb... Read 17683 atoms Analyzing pdb file Splitting PDB chains based on TER records or changing chain id. There are 1 chains and 0 blocks of water and 256 residues with 17683 atoms chain #res #atoms 1 ' ' 2641 17683 All occupancies are one Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/atomtypes.atp Atomtype 1 Reading residue database... (charmm36) Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/aminoacids.rtp Residue 41 Sorting it all out... Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/dna.rtp Residue 53 Sorting it all out... Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/lipids.rtp Residue 89 Sorting it all out... Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/rna.rtp Residue 101 Sorting it all out... Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/aminoacids.hdb Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/lipids.hdb Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/aminoacids.n.tdb Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/aminoacids.c.tdb Processing chain 1 (17683 atoms, 2641 residues) There are 80 donors and 0 acceptors There are 0 hydrogen bonds Warning: Starting residue POPE1 in chain not identified as Protein/RNA/DNA. Warning: Starting residue POPE2 in chain not identified as Protein/RNA/DNA. Warning: Starting residue POPE3 in chain not identified as Protein/RNA/DNA. Warning: Starting residue POPE4 in chain not identified as Protein/RNA/DNA. Warning: Starting residue POPE5 in chain not identified as Protein/RNA/DNA. More than 5 unidentified residues at start of chain - disabling further warnings. 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 Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/aminoacids.arn Checking for duplicate atoms.... Now there are 2641 residues with 17683 atoms Making bonds... Number of bonds was 17603, now 17603 Generating angles, dihedrals and pairs... Before cleaning: 26320 pairs Before cleaning: 26320 dihedrals Keeping all generated dihedrals Making cmap torsions...There are 26320 dihedrals, 160 impropers, 26723 angles 26320 pairs, 17603 bonds and 0 virtual sites Total mass 103578.495 a.m.u. Total charge 0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: pope80-c36npt.pdb. The Charmm36 force field and the tips3p water model are used. --------- ETON ESAELP ------------ ### # pope.top ### ; ; File 'pope.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Mon May 23 17:31:33 2011 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.3 ; ; Command line was: ; pdb2gmx -f pope80-c36npt.pdb -o pope.pdb -p pope.top -ff charmm36 ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include "charmm36.ff/forcefield.itp" [ moleculetype ] ; Name nrexcl Other 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 POPE rtp POPE q 0.0 1 NH3L 1 POPE N 1 -0.3 14.007 ; qtot -0.3 2 HCL 1 POPE HN1 2 0.33 1.008 ; qtot 0.03 3 HCL 1 POPE HN2 3 0.33 1.008 ; qtot 0.36 4 HCL 1 POPE HN3 4 0.33 1.008 ; qtot 0.69 5 CTL2 1 POPE C12 5 0.13 12.011 ; qtot 0.82 6 HAL2 1 POPE H12A 6 0.09 1.008 ; qtot 0.91 7 HAL2 1 POPE H12B 7 0.09 1.008 ; qtot 1 8 CTL2 1 POPE C11 8 -0.08 12.011 ; qtot 0.92 9 HAL2 1 POPE H11A 9 0.09 1.008 ; qtot 1.01 10 HAL2 1 POPE H11B 10 0.09 1.008 ; qtot 1.1 11 PL 1 POPE P 11 1.5 30.974 ; qtot 2.6 12 O2L 1 POPE O13 12 -0.78 15.9994 ; qtot 1.82 13 O2L 1 POPE O14 13 -0.78 15.9994 ; qtot 1.04 14 OSLP 1 POPE O11 14 -0.57 15.9994 ; qtot 0.47 15 OSLP 1 POPE O12 15 -0.57 15.9994 ; qtot -0.1 16 CTL2 1 POPE C1 16 -0.08 12.011 ; qtot -0.18 17 HAL2 1 POPE HA 17 0.09 1.008 ; qtot -0.09 18 HAL2 1 POPE HB 18 0.09 1.008 ; qtot 0 19 CTL1 1 POPE C2 19 0.17 12.011 ; qtot 0.17 20 HAL1 1 POPE HS 20 0.09 1.008 ; qtot 0.26 21 OSL 1 POPE O21 21 -0.49 15.9994 ; qtot -0.23 22 CL 1 POPE C21 22 0.9 12.011 ; qtot 0.67 23 OBL 1 POPE O22 23 -0.63 15.9994 ; qtot 0.04 24 CTL2 1 POPE C22 24 -0.22 12.011 ; qtot -0.18 25 HAL2 1 POPE H2R 25 0.09 1.008 ; qtot -0.09 26 HAL2 1 POPE H2S 26 0.09 1.008 ; qtot 0 27 CTL2 1 POPE C3 27 0.08 12.011 ; qtot 0.08 28 HAL2 1 POPE HX 28 0.09 1.008 ; qtot 0.17 29 HAL2 1 POPE HY 29 0.09 1.008 ; qtot 0.26 30 OSL 1 POPE O31 30 -0.49 15.9994 ; qtot -0.23 31 CL 1 POPE C31 31 0.9 12.011 ; qtot 0.67 32 OBL 1 POPE O32 32 -0.63 15.9994 ; qtot 0.04 33 CTL2 1 POPE C32 33 -0.22 12.011 ; qtot -0.18 34 HAL2 1 POPE H2X 34 0.09 1.008 ; qtot -0.09 35 HAL2 1 POPE H2Y 35 0.09 1.008 ; qtot 0 36 CTL2 1 POPE C23 36 -0.18 12.011 ; qtot -0.18 37 HAL2 1 POPE H3R 37 0.09 1.008 ; qtot -0.09 38 HAL2 1 POPE H3S 38 0.09 1.008 ; qtot 0 39 CTL2 1 POPE C24 39 -0.18 12.011 ; qtot -0.18 40 HAL2 1 POPE H4R 40 0.09 1.008 ; qtot -0.09 41 HAL2 1 POPE H4S 41 0.09 1.008 ; qtot 0 42 CTL2 1 POPE C25 42 -0.18 12.011 ; qtot -0.18 43 HAL2 1 POPE H5R 43 0.09 1.008 ; qtot -0.09 44 HAL2 1 POPE H5S 44 0.09 1.008 ; qtot 0 45 CTL2 1 POPE C26 45 -0.18 12.011 ; qtot -0.18 46 HAL2 1 POPE H6R 46 0.09 1.008 ; qtot -0.09 47 HAL2 1 POPE H6S 47 0.09 1.008 ; qtot 0 48 CTL2 1 POPE C27 48 -0.18 12.011 ; qtot -0.18 49 HAL2 1 POPE H7R 49 0.09 1.008 ; qtot -0.09 50 HAL2 1 POPE H7S 50 0.09 1.008 ; qtot 0 51 CTL2 1 POPE C28 51 -0.18 12.011 ; qtot -0.18 52 HAL2 1 POPE H8R 52 0.09 1.008 ; qtot -0.09 53 HAL2 1 POPE H8S 53 0.09 1.008 ; qtot 0 54 CEL1 1 POPE C29 54 -0.15 12.011 ; qtot -0.15 55 HEL1 1 POPE H91 55 0.15 1.008 ; qtot 0 56 CEL1 1 POPE C210 56 -0.15 12.011 ; qtot -0.15 57 HEL1 1 POPE H101 57 0.15 1.008 ; qtot 0 58 CTL2 1 POPE C211 58 -0.18 12.011 ; qtot -0.18 59 HAL2 1 POPE H11R 59 0.09 1.008 ; qtot -0.09 60 HAL2 1 POPE H11S 60 0.09 1.008 ; qtot 0 61 CTL2 1 POPE C212 61 -0.18 12.011 ; qtot -0.18 62 HAL2 1 POPE H12R 62 0.09 1.008 ; qtot -0.09 63 HAL2 1 POPE H12S 63 0.09 1.008 ; qtot 0 64 CTL2 1 POPE C213 64 -0.18 12.011 ; qtot -0.18 65 HAL2 1 POPE H13R 65 0.09 1.008 ; qtot -0.09 66 HAL2 1 POPE H13S 66 0.09 1.008 ; qtot 0 67 CTL2 1 POPE C214 67 -0.18 12.011 ; qtot -0.18 68 HAL2 1 POPE H14R 68 0.09 1.008 ; qtot -0.09 69 HAL2 1 POPE H14S 69 0.09 1.008 ; qtot 0 70 CTL2 1 POPE C215 70 -0.18 12.011 ; qtot -0.18 71 HAL2 1 POPE H15R 71 0.09 1.008 ; qtot -0.09 72 HAL2 1 POPE H15S 72 0.09 1.008 ; qtot 0 73 CTL2 1 POPE C216 73 -0.18 12.011 ; qtot -0.18 74 HAL2 1 POPE H16R 74 0.09 1.008 ; qtot -0.09 75 HAL2 1 POPE H16S 75 0.09 1.008 ; qtot 0 76 CTL2 1 POPE C217 76 -0.18 12.011 ; qtot -0.18 77 HAL2 1 POPE H17R 77 0.09 1.008 ; qtot -0.09 78 HAL2 1 POPE H17S 78 0.09 1.008 ; qtot 0 79 CTL3 1 POPE C218 79 -0.27 12.011 ; qtot -0.27 80 HAL3 1 POPE H18R 80 0.09 1.008 ; qtot -0.18 81 HAL3 1 POPE H18S 81 0.09 1.008 ; qtot -0.09 82 HAL3 1 POPE H18T 82 0.09 1.008 ; qtot 0 83 CTL2 1 POPE C33 83 -0.18 12.011 ; qtot -0.18 84 HAL2 1 POPE H3X 84 0.09 1.008 ; qtot -0.09 85 HAL2 1 POPE H3Y 85 0.09 1.008 ; qtot 0 86 CTL2 1 POPE C34 86 -0.18 12.011 ; qtot -0.18 87 HAL2 1 POPE H4X 87 0.09 1.008 ; qtot -0.09 88 HAL2 1 POPE H4Y 88 0.09 1.008 ; qtot 0 89 CTL2 1 POPE C35 89 -0.18 12.011 ; qtot -0.18 90 HAL2 1 POPE H5X 90 0.09 1.008 ; qtot -0.09 91 HAL2 1 POPE H5Y 91 0.09 1.008 ; qtot 0 92 CTL2 1 POPE C36 92 -0.18 12.011 ; qtot -0.18 93 HAL2 1 POPE H6X 93 0.09 1.008 ; qtot -0.09 94 HAL2 1 POPE H6Y 94 0.09 1.008 ; qtot 0 95 CTL2 1 POPE C37 95 -0.18 12.011 ; qtot -0.18 96 HAL2 1 POPE H7X 96 0.09 1.008 ; qtot -0.09 97 HAL2 1 POPE H7Y 97 0.09 1.008 ; qtot 0 98 CTL2 1 POPE C38 98 -0.18 12.011 ; qtot -0.18 99 HAL2 1 POPE H8X 99 0.09 1.008 ; qtot -0.09 100 HAL2 1 POPE H8Y 100 0.09 1.008 ; qtot 0 101 CTL2 1 POPE C39 101 -0.18 12.011 ; qtot -0.18 102 HAL2 1 POPE H9X 102 0.09 1.008 ; qtot -0.09 103 HAL2 1 POPE H9Y 103 0.09 1.008 ; qtot 0 104 CTL2 1 POPE C310 104 -0.18 12.011 ; qtot -0.18 105 HAL2 1 POPE H10X 105 0.09 1.008 ; qtot -0.09 106 HAL2 1 POPE H10Y 106 0.09 1.008 ; qtot 0 107 CTL2 1 POPE C311 107 -0.18 12.011 ; qtot -0.18 108 HAL2 1 POPE H11X 108 0.09 1.008 ; qtot -0.09 109 HAL2 1 POPE H11Y 109 0.09 1.008 ; qtot 0 110 CTL2 1 POPE C312 110 -0.18 12.011 ; qtot -0.18 111 HAL2 1 POPE H12X 111 0.09 1.008 ; qtot -0.09 112 HAL2 1 POPE H12Y 112 0.09 1.008 ; qtot 0 113 CTL2 1 POPE C313 113 -0.18 12.011 ; qtot -0.18 114 HAL2 1 POPE H13X 114 0.09 1.008 ; qtot -0.09 115 HAL2 1 POPE H13Y 115 0.09 1.008 ; qtot 0 116 CTL2 1 POPE C314 116 -0.18 12.011 ; qtot -0.18 117 HAL2 1 POPE H14X 117 0.09 1.008 ; qtot -0.09 118 HAL2 1 POPE H14Y 118 0.09 1.008 ; qtot 0 119 CTL2 1 POPE C315 119 -0.18 12.011 ; qtot -0.18 120 HAL2 1 POPE H15X 120 0.09 1.008 ; qtot -0.09 121 HAL2 1 POPE H15Y 121 0.09 1.008 ; qtot 0 122 CTL3 1 POPE C316 122 -0.27 12.011 ; qtot -0.27 123 HAL3 1 POPE H16X 123 0.09 1.008 ; qtot -0.18 124 HAL3 1 POPE H16Y 124 0.09 1.008 ; qtot -0.09 125 HAL3 1 POPE H16Z 125 0.09 1.008 ; qtot 0 ; residue 2 POPE rtp POPE q 0.0 126 NH3L 2 POPE N 126 -0.3 14.007 ; qtot -0.3 127 HCL 2 POPE HN1 127 0.33 1.008 ; qtot 0.03 128 HCL 2 POPE HN2 128 0.33 1.008 ; qtot 0.36 129 HCL 2 POPE HN3 129 0.33 1.008 ; qtot 0.69 ... ; residue 256 TIP3 rtp TIP3 q 0.0 17678 OT 2560 TIP3 OH2 12560 -0.834 15.9994 ; qtot -0.834 17679 HT 2560 TIP3 H1 12560 0.417 1.008 ; qtot -0.417 17680 HT 2560 TIP3 H2 12560 0.417 1.008 ; qtot 0 ... [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 5 7 1 .... 9995 9999 1 9995 10000 1 9996 9998 1 9996 9999 1 9996 10000 1 [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 3 5 2 1 4 5 2 1 5 5 3 1 4 5 3 1 5 5 4 1 5 5 .... 17678 17679 17680 5 17678 17680 17679 5 17682 17681 17683 5 17681 17682 17683 5 17681 17683 17682 5 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 2 1 5 6 9 2 1 5 7 9 2 1 5 8 9 3 1 5 6 9 3 1 5 7 9 3 1 5 8 9 4 1 5 6 9 4 1 5 7 9 4 1 5 8 9 1 5 8 9 9 .... 9772 9771 9774 9773 2 9781 9780 9783 9782 2 9897 9896 9899 9898 2 9906 9905 9908 9907 2 ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "charmm36.ff/tips3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "charmm36.ff/ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound #mols Other 1 -- 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! 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