[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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