[gmx-users] struggles with cyclic peptides
Nikhil
scinikhil at gmail.com
Sun Sep 13 20:40:06 CEST 2015
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
-------------------------------------------------------
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
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