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

Nikhil Maroli scinikhil at gmail.com
Fri Sep 11 19:39:52 CEST 2015


*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


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