[gmx-users] Charmm36 in Gromacs: missing dihedrals
Jon Fuller
jonathan.fuller at gmail.com
Wed May 25 15:49:38 CEST 2011
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 <jalemkul at 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
>
> ========================================
> --
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