[gmx-users] struggles with cyclic peptides

Justin Lemkul jalemkul at vt.edu
Mon Sep 14 12:15:16 CEST 2015



On 9/13/15 2:39 PM, Nikhil wrote:
> with -missing flag also unable to use None terminals it shows error here
> is the full output of pdb2gmx
>   pdb2gmx -f cpn.pdb -ter -missing
>
>
> Select the Force Field:
>  From '/usr/share/gromacs/top':
>   1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
> 1999-2012, 2003)
>   2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
>   3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res.
> 29, 461-469, 1996)
>   4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21,
> 1049-1074, 2000)
>   5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-
> 725, 2006)
>   6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al.,
> Proteins 78, 1950-58, 2010)
>   7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
>   8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
>   9: GROMOS96 43a1 force field
> 10: GROMOS96 43a2 force field (improved alkane dihedrals)
> 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
> 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
> 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> 14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856,
> DOI: 10.1007/s00249-011-0700-9)
> 15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> 8
>
> 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 1 chains and 0 blocks of water and 4 residues with 67 atoms
>
>    chain  #res #atoms
>    1 'A'     4     67
>
> 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.5#
> Processing chain 1 'A' (67 atoms, 4 residues)
> Identified residue ALA1 as a starting terminus.
> Identified residue LYS4 as a ending terminus.
> 9 out of 9 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
>                      ALA1
>                        N1
>      LYS4     C51   0.134
> Linking ALA-1 N-1 and LYS-4 C-51...
> Select start terminus type for ALA-1
>   0: NH3+
>   1: NH2
>   2: None
> 2
> Start terminus ALA-1: None
> Select end terminus type for LYS-4
>   0: COO-
>   1: COOH
>   2: CT2
>   3: CT3
>   4: None
> 4
> End terminus LYS-4: 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
> -------------------------------------------------------
>

Indeed it seems at present there is no way for pdb2gmx to generate this 
topology.  Cyclic peptides have never been handled cleanly in GROMACS; it's 
probably something we should add at some point, but it all comes down to 
someone's willingness to code it. Any volunteers? :)

-Justin

>
>
> here im putting the pdb file of my structure
>
> 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 A   2      -4.781   0.766   0.348  1.00  0.00
> N
> ATOM     12  H   LEU A   2      -3.776   0.718   0.265  1.00  0.00
> H
> ATOM     13  CA  LEU A   2      -5.549   0.859  -0.902  1.00  0.00
> C
> ATOM     14  HA  LEU A   2      -6.305   1.635  -0.790  1.00  0.00
> H
> ATOM     15  C   LEU A   2      -6.247  -0.477  -1.208  1.00  0.00
> C
> ATOM     16  O   LEU A   2      -5.673  -1.538  -0.993  1.00  0.00
> O
> ATOM     17  CB  LEU A   2      -4.589   1.279  -2.034  1.00  0.00
> C
> ATOM     18 HB1  LEU A   2      -4.111   2.220  -1.754  1.00  0.00
> H
> ATOM     19 HB1  LEU A   2      -3.807   0.520  -2.117  1.00  0.00
> H
> ATOM     20  CG  LEU A   2      -5.238   1.454  -3.426  1.00  0.00
> C
> ATOM     21  HG  LEU A   2      -5.676   0.505  -3.738  1.00  0.00
> H
> ATOM     22  CD1 LEU A   2      -6.340   2.525  -3.427  1.00  0.00
> C
> ATOM     23 HD11 LEU A   2      -6.723   2.656  -4.440  1.00  0.00
> H
> ATOM     24 HD12 LEU A   2      -5.940   3.476  -3.074  1.00  0.00
> H
> ATOM     25 HD13 LEU A   2      -7.169   2.224  -2.789  1.00  0.00
> H
> ATOM     26  CD2 LEU A   2      -4.160   1.833  -4.450  1.00  0.00
> C
> ATOM     27 HD21 LEU A   2      -4.605   1.920  -5.442  1.00  0.00
> H
> ATOM     28 HD22 LEU A   2      -3.391   1.060  -4.482  1.00  0.00
> H
> ATOM     29 HD23 LEU A   2      -3.700   2.785  -4.180  1.00  0.00
> H
> ATOM     30  N   GLN A   3      -7.497  -0.424  -1.671  1.00  0.00
> N
> ATOM     31  H   GLN A   3      -7.910   0.469  -1.882  1.00  0.00
> H
> ATOM     32  CA  GLN A   3      -8.323  -1.613  -1.897  1.00  0.00
> C
> ATOM     33  HA  GLN A   3      -8.020  -2.397  -1.198  1.00  0.00
> H
> ATOM     34  C   GLN A   3      -9.820  -1.324  -1.624  1.00  0.00
> C
> ATOM     35  O   GLN A   3     -10.666  -1.591  -2.471  1.00  0.00
> O
> ATOM     36  CB  GLN A   3      -8.045  -2.130  -3.325  1.00  0.00
> C
> ATOM     37 HB1  GLN A   3      -8.470  -1.427  -4.044  1.00  0.00
> H
> ATOM     38 HB2  GLN A   3      -6.967  -2.154  -3.497  1.00  0.00
> H
> ATOM     39  CG  GLN A   3      -8.587  -3.552  -3.580  1.00  0.00
> C
> ATOM     40 HG1  GLN A   3      -7.751  -4.250  -3.637  1.00  0.00
> H
> ATOM     41 HG1  GLN A   3      -9.225  -3.868  -2.754  1.00  0.00
> H
> ATOM     42  CD  GLN A   3      -9.400  -3.641  -4.869  1.00  0.00
> C
> ATOM     43  OE1 GLN A   3      -8.993  -4.228  -5.857  1.00  0.00
> O
> ATOM     44  NE2 GLN A   3     -10.567  -3.038  -4.913  1.00  0.00
> N
> ATOM     45 HE21 GLN A   3     -11.082  -3.101  -5.769  1.00  0.00
> H
> ATOM     46 HE22 GLN A   3     -10.883  -2.515  -4.103  1.00  0.00
> H
> ATOM     47  N   LYS A   4     -10.243  -0.726  -0.500  1.00  0.00
> N
> ATOM     48  H   LYS A   4     -11.247  -0.617  -0.471  1.00  0.00
> H
> ATOM     49  CA  LYS A   4      -9.503  -0.233   0.679  1.00  0.00
> C
> ATOM     50  HA  LYS A   4      -8.973   0.661   0.371  1.00  0.00
> H
> ATOM     51  C   LYS A   4      -8.483  -1.241   1.259  1.00  0.00
> C
> ATOM     52  O   LYS A   4      -8.735  -2.437   1.259  1.00  0.00
> O
> ATOM     53  CB  LYS A   4     -10.517   0.166   1.774  1.00  0.00
> C
> ATOM     54 HB1  LYS A   4     -11.377  -0.504   1.744  1.00  0.00
> H
> ATOM     55 HB2  LYS A   4     -10.054   0.023   2.751  1.00  0.00
> H
> ATOM     56  CG  LYS A   4     -10.987   1.632   1.713  1.00  0.00
> C
> ATOM     57 HG1  LYS A   4     -11.669   1.806   2.546  1.00  0.00
> H
> ATOM     58 HG2  LYS A   4     -10.120   2.277   1.858  1.00  0.00
> H
> ATOM     59  CD  LYS A   4     -11.688   2.059   0.416  1.00  0.00
> C
> ATOM     60 HD1  LYS A   4     -11.973   3.108   0.503  1.00  0.00
> H
> ATOM     61 HD2  LYS A   4     -10.998   1.963  -0.422  1.00  0.00
> H
> ATOM     62  CE  LYS A   4     -12.942   1.228   0.144  1.00  0.00
> C
> ATOM     63 HE1  LYS A   4     -12.670   0.176   0.087  1.00  0.00
> H
> ATOM     64 HE2  LYS A   4     -13.661   1.373   0.949  1.00  0.00
> H
> ATOM     65  NZ  LYS A   4     -13.559   1.618  -1.126  1.00  0.00
> N
> ATOM     66 HZ1  LYS A   4     -14.307   0.974  -1.341  1.00  0.00
> H
> ATOM     67 HZ2  LYS A   4     -13.944   2.548  -1.040  1.00  0.00
> H
> TER      68      LYS A   4
> CONECT    1    2    3   51
> CONECT   51    1   49   52
> END
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================


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