Dear Mark and Justin, Thanks for the quick reply. I must have misunderstood the procedure. I was assuming that the generated top file should include the actual values used for the Urea-Bradley terms. Previously I have only included molecules using an itp file and was expecting similar behaviour.
For anyone interested. I got the system to work by removing the waters from the input file and running pdb2gmx. Then using editconf on the pdb with waters. Then I manually edited the top file to add the correct number of water molecules into the [ molecules ] directive. Then I needed to rename the water molecules correctly to correspond to the correct names in the tips3p.itp file in the charmm36 directory. Following this I ran grompp successfully. Many thanks, Jon On 25 May 2011 14:20, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Jon Fuller wrote: >> >> 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. >> > > I see no problem here. You have all the necessary directives ([bonds], > [angles], and [dihedrals]) in the .top you show. The actual parameters for > those bonded terms are not written to the .top; they are taken from > ffbonded.itp when running grompp. Now, if grompp complains about something > being missing, that's a separate issue. > > -Justin > >> 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 > > -- > ======================================== > > 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 > -- 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. 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