[gmx-users] Cyclic peptide by using specbond.dat
João M. Damas
jmdamas at itqb.unl.pt
Fri Sep 11 22:45:19 CEST 2015
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!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
--
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
More information about the gromacs.org_gmx-users
mailing list