[gmx-users] Cyclic peptide by using specbond.dat

Mark Abraham mark.j.abraham at gmail.com
Fri Sep 11 23:15:51 CEST 2015


Hi,

Yes, that's exactly what parts of the output are saying.

Mark

On Fri, 11 Sep 2015 22:45 João M. Damas <jmdamas at itqb.unl.pt> wrote:

> This does not seem related with specbond.dat, but rather a problem with the
> chains: each residue is a different chain and maybe that is causing
> troubles with the termini. Remove the chain ID or make them all chain A.
>
> João
>
> On Fri, Sep 11, 2015 at 6:39 PM, Nikhil Maroli <scinikhil at gmail.com>
> wrote:
>
> > *Dear Gromacs users*
> > *i have been having a bit of issues generating accurate topology for
> cyclic
> > peptide*
> >
> > *i added extra terms in specbond.dat (Last Line)*
> > *as *
> >
> > 9
> >
> > CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
> >
> > CYS SG 1 HEM FE 2 0.25 CYS2 HEME
> >
> > CYS SG 1 HEM CAB 1 0.18 CYS2 HEME
> >
> > CYS SG 1 HEM CAC 1 0.18 CYS2 HEME
> >
> > HIS NE2 1 HEM FE 1 0.2 HIS1 HEME
> >
> > MET SD 1 HEM FE 1 0.24 MET HEME
> >
> > CO      C       1       HEME    FE      1       0.19    CO      HEME
> > CYM     SG      1       CYM     SG      1       0.2     CYS2    CYS2
> >
> > *LYS C 1 ALA N 1 0.135 LYS ALA*
> >
> >
> > and my pdb file is as
> > SEQRES   1 A    4  ALA LEU GLN LYS
> > LINK         N   ALA A   1                 C   LYS A   4
> >  1.34
> > ATOM      1  N   ALA A   1      -7.317  -0.819   1.765  1.00  0.00
> >   N
> > ATOM      2  H   ALA A   1      -6.725  -1.565   2.103  1.00  0.00
> >   H
> > ATOM      3  CA  ALA A   1      -6.768   0.542   1.865  1.00  0.00
> >   C
> > ATOM      4  HA  ALA A   1      -7.224   1.212   1.142  1.00  0.00
> >   H
> > ATOM      5  C   ALA A   1      -5.244   0.544   1.585  1.00  0.00
> >   C
> > ATOM      6  O   ALA A   1      -4.449   0.351   2.495  1.00  0.00
> >   O
> > ATOM      7  CB  ALA A   1      -7.092   1.097   3.262  1.00  0.00
> >   C
> > ATOM      8 HB1  ALA A   1      -6.673   0.442   4.029  1.00  0.00
> >   H
> > ATOM      9 HB1  ALA A   1      -8.168   1.171   3.407  1.00  0.00
> >   H
> > ATOM     10 HB1  ALA A   1      -6.651   2.089   3.375  1.00  0.00
> >   H
> > ATOM     11  N   LEU B   2      -4.781   0.766   0.348  1.00  0.00
> >   N
> > ATOM     12  H   LEU B   2      -3.776   0.718   0.265  1.00  0.00
> >   H
> > ATOM     13  CA  LEU B   2      -5.549   0.859  -0.902  1.00  0.00
> >   C
> > ATOM     14  HA  LEU B   2      -6.305   1.635  -0.790  1.00  0.00
> >   H
> > ATOM     15  C   LEU B   2      -6.247  -0.477  -1.208  1.00  0.00
> >   C
> > ATOM     16  O   LEU B   2      -5.673  -1.538  -0.993  1.00  0.00
> >   O
> > ATOM     17  CB  LEU B   2      -4.589   1.279  -2.034  1.00  0.00
> >   C
> > ATOM     18 HB1  LEU B   2      -4.111   2.220  -1.754  1.00  0.00
> >   H
> > ATOM     19 HB1  LEU B   2      -3.807   0.520  -2.117  1.00  0.00
> >   H
> > ATOM     20  CG  LEU B   2      -5.238   1.454  -3.426  1.00  0.00
> >   C
> > ATOM     21  HG  LEU B   2      -5.676   0.505  -3.738  1.00  0.00
> >   H
> > ATOM     22  CD1 LEU B   2      -6.340   2.525  -3.427  1.00  0.00
> >   C
> > ATOM     23 HD11 LEU B   2      -6.723   2.656  -4.440  1.00  0.00
> >   H
> > ATOM     24 HD12 LEU B   2      -5.940   3.476  -3.074  1.00  0.00
> >   H
> > ATOM     25 HD13 LEU B   2      -7.169   2.224  -2.789  1.00  0.00
> >   H
> > ATOM     26  CD2 LEU B   2      -4.160   1.833  -4.450  1.00  0.00
> >   C
> > ATOM     27 HD21 LEU B   2      -4.605   1.920  -5.442  1.00  0.00
> >   H
> > ATOM     28 HD22 LEU B   2      -3.391   1.060  -4.482  1.00  0.00
> >   H
> > ATOM     29 HD23 LEU B   2      -3.700   2.785  -4.180  1.00  0.00
> >   H
> > ATOM     30  N   GLN C   3      -7.497  -0.424  -1.671  1.00  0.00
> >   N
> > ATOM     31  H   GLN C   3      -7.910   0.469  -1.882  1.00  0.00
> >   H
> > ATOM     32  CA  GLN C   3      -8.323  -1.613  -1.897  1.00  0.00
> >   C
> > ATOM     33  HA  GLN C   3      -8.020  -2.397  -1.198  1.00  0.00
> >   H
> > ATOM     34  C   GLN C   3      -9.820  -1.324  -1.624  1.00  0.00
> >   C
> > ATOM     35  O   GLN C   3     -10.666  -1.591  -2.471  1.00  0.00
> >   O
> > ATOM     36  CB  GLN C   3      -8.045  -2.130  -3.325  1.00  0.00
> >   C
> > ATOM     37 HB1  GLN C   3      -8.470  -1.427  -4.044  1.00  0.00
> >   H
> > ATOM     38 HB2  GLN C   3      -6.967  -2.154  -3.497  1.00  0.00
> >   H
> > ATOM     39  CG  GLN C   3      -8.587  -3.552  -3.580  1.00  0.00
> >   C
> > ATOM     40 HG1  GLN C   3      -7.751  -4.250  -3.637  1.00  0.00
> >   H
> > ATOM     41 HG1  GLN C   3      -9.225  -3.868  -2.754  1.00  0.00
> >   H
> > ATOM     42  CD  GLN C   3      -9.400  -3.641  -4.869  1.00  0.00
> >   C
> > ATOM     43  OE1 GLN C   3      -8.993  -4.228  -5.857  1.00  0.00
> >   O
> > ATOM     44  NE2 GLN C   3     -10.567  -3.038  -4.913  1.00  0.00
> >   N
> > ATOM     45 HE21 GLN C   3     -11.082  -3.101  -5.769  1.00  0.00
> >   H
> > ATOM     46 HE22 GLN C   3     -10.883  -2.515  -4.103  1.00  0.00
> >   H
> > ATOM     47  N   LYS D   4     -10.243  -0.726  -0.500  1.00  0.00
> >   N
> > ATOM     48  H   LYS D   4     -11.247  -0.617  -0.471  1.00  0.00
> >   H
> > ATOM     49  CA  LYS D   4      -9.503  -0.233   0.679  1.00  0.00
> >   C
> > ATOM     50  HA  LYS D   4      -8.973   0.661   0.371  1.00  0.00
> >   H
> > ATOM     51  C   LYS D   4      -8.483  -1.241   1.259  1.00  0.00
> >   C
> > ATOM     52  O   LYS D   4      -8.735  -2.437   1.259  1.00  0.00
> >   O
> > ATOM     53  CB  LYS D   4     -10.517   0.166   1.774  1.00  0.00
> >   C
> > ATOM     54 HB1  LYS D   4     -11.377  -0.504   1.744  1.00  0.00
> >   H
> > ATOM     55 HB2  LYS D   4     -10.054   0.023   2.751  1.00  0.00
> >   H
> > ATOM     56  CG  LYS D   4     -10.987   1.632   1.713  1.00  0.00
> >   C
> > ATOM     57 HG1  LYS D   4     -11.669   1.806   2.546  1.00  0.00
> >   H
> > ATOM     58 HG2  LYS D   4     -10.120   2.277   1.858  1.00  0.00
> >   H
> > ATOM     59  CD  LYS D   4     -11.688   2.059   0.416  1.00  0.00
> >   C
> > ATOM     60 HD1  LYS D   4     -11.973   3.108   0.503  1.00  0.00
> >   H
> > ATOM     61 HD2  LYS D   4     -10.998   1.963  -0.422  1.00  0.00
> >   H
> > ATOM     62  CE  LYS D   4     -12.942   1.228   0.144  1.00  0.00
> >   C
> > ATOM     63 HE1  LYS D   4     -12.670   0.176   0.087  1.00  0.00
> >   H
> > ATOM     64 HE2  LYS D   4     -13.661   1.373   0.949  1.00  0.00
> >   H
> > ATOM     65  NZ  LYS D   4     -13.559   1.618  -1.126  1.00  0.00
> >   N
> > ATOM     66 HZ1  LYS D   4     -14.307   0.974  -1.341  1.00  0.00
> >   H
> > ATOM     67 HZ2  LYS D   4     -13.944   2.548  -1.040  1.00  0.00
> >   H
> > TER      68      LYS D   4
> > CONECT    1    2    3   51
> > CONECT   51    1   49   52
> > END
> >
> >
> >
> > *After i giving the command pdb2gmx -f  abc.pdb -ter *
> > *and selecting Terminals 'None'*
> >
> > *forcefield selected is charmm27 and water model is TIP3P (specbond.dat
> is
> > in working directory)*
> > *im getting an error as*
> >
> > *Using the Charmm27 force field in directory charmm27.ff*
> >
> > Opening force field file
> /usr/share/gromacs/top/charmm27.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: TIP5P   TIP 5-point (see http://redmine.gromacs.org/issues/1348 for
> > issues)
> >  5: SPC     simple point charge
> >  6: SPC/E   extended simple point charge
> >  7: None
> > 1
> > Opening force field file
> /usr/share/gromacs/top/charmm27.ff/aminoacids.r2b
> > Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.r2b
> > Reading cpn.pdb...
> > WARNING: all CONECT records are ignored
> > Read 67 atoms
> > Analyzing pdb file
> > Splitting chemical chains based on TER records or chain id changing.
> > There are 4 chains and 0 blocks of water and 4 residues with 67 atoms
> >
> >   chain  #res #atoms
> >   1 'A'     1     10
> >   2 'B'     1     19
> >   3 'C'     1     17
> >   4 'D'     1     21
> >
> > All occupancies are one
> > Opening force field file /usr/share/gromacs/top/charmm27.ff/atomtypes.atp
> > Atomtype 213
> > Reading residue database... (charmm27)
> > Opening force field file
> /usr/share/gromacs/top/charmm27.ff/aminoacids.rtp
> > Residue 44
> > Sorting it all out...
> > Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.rtp
> > Residue 48
> > Sorting it all out...
> > Opening force field file /usr/share/gromacs/top/charmm27.ff/lipids.rtp
> > Residue 60
> > Sorting it all out...
> > Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.rtp
> > Residue 64
> > Sorting it all out...
> > Opening force field file
> /usr/share/gromacs/top/charmm27.ff/aminoacids.hdb
> > Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.hdb
> > Opening force field file /usr/share/gromacs/top/charmm27.ff/lipids.hdb
> > Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.hdb
> > Opening force field file
> > /usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb
> > Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.n.tdb
> > Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.n.tdb
> > Opening force field file
> > /usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb
> > Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.c.tdb
> > Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.c.tdb
> >
> >
> > Back Off! I just backed up topol.top to ./#topol.top.2#
> > Processing chain 1 'A' (10 atoms, 1 residues)
> > Identified residue ALA1 as a starting terminus.
> > Identified residue ALA1 as a ending terminus.
> > 9 out of 9 lines of specbond.dat converted successfully
> > Select start terminus type for ALA-1
> >  0: NH3+
> >  1: NH2
> >  2: None
> > 2
> > Start terminus ALA-1: None
> > Select end terminus type for ALA-1
> >  0: COO-
> >  1: COOH
> >  2: CT2
> >  3: CT3
> >  4: None
> > 4
> > End terminus ALA-1: None
> >
> > -------------------------------------------------------
> > Program pdb2gmx, VERSION 5.0.2
> > Source code file:
> > /build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/pdb2top.cpp, line:
> > 1091
> >
> > *Fatal error:*
> > *There is a dangling bond at at least one of the terminal ends. Fix your
> > coordinate file, add a new terminal database entry (.tdb), or select the
> > proper existing terminal entry.*
> > *For more information and tips for troubleshooting, please check the
> > GROMACS*
> > *website at http://www.gromacs.org/Documentation/Errors
> > <http://www.gromacs.org/Documentation/Errors>*
> >
> >
> >
> > i hope someone can guide me how excactly the specbond.dat option can use
> >
> > Ragards,
> > Nikhil Maroli
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
>
>
>
> --
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
> --
> Gromacs Users mailing list
>
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> posting!
>
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>
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