[gmx-users] Charmm36 in Gromacs: missing dihedrals
Justin A. Lemkul
jalemkul at vt.edu
Wed May 25 14:20:23 CEST 2011
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
========================================
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