[gmx-users] Problem fpr building a peptide with two modified residues with amber ff

Sun Jan 14 16:04:29 CET 2018

Hi Justin

I have added the TYO and MER residue as Protein is the residuetypes.dat. And the the following output with pdb2gmx. I select 2 and 6

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  gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o Atosiban_amber14sb.pdb -i Atosiban_posre.itp -rtpres yes

Select the Force Field:
From '/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top/':
 1: Amber12sb ff99SB + new backbone and side chain torsion for protein
 2: AMBER14SB_parmbsc1 (ff14SB for protein + parmbsc1 for DNA)
 3: AMBER94 BCL force field (J. Comp. Chem. 2012, 33, 1969–1980)
 4: CHARMM36 all-atom force field (July 2017)
 5: CHARMM36 all-atom force field, surfactants and pigments
 6: GLYCAM06 force field for alkylglycosides and RG1 (2011, J. Phys. Chem. B 2011, 115, 487-499 )
 7: GROMOS96 2016H66 force field (J. Chem. Theory. Comput., 2016, 12, 3825−3850)
 8: GROMOS96 53a6 force field with PVP (JCC 2004 vol 25 pag 1656 and J. Phys. Chem. C, 2015, 119 (14), pp 7888–7899)
 9: GROMOS96 53a6carbo force field (JCC 2011 vol 32 pag 998, doi 10.1002/jcc.21675)
10: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
From '/ccc/products/gromacs-5.1.2/default/share/gromacs/top':
11: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
12: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
13: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
14: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
15: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
16: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
17: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
18: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
19: GROMOS96 43a1 force field
20: GROMOS96 43a2 force field (improved alkane dihedrals)
21: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
22: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
23: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
24: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
25: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
2

Using the Amber14sb_parmbsc1 force field in directory /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff

Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/watermodels.dat

Select the Water Model:
 1: TIP3P     TIP 3-point, recommended
 2: TIP4P     TIP 4-point
 3: TIP4P-Ew  TIP 4-point optimized with Ewald
 4: SPC       simple point charge
 5: SPC/E     extended simple point charge
 6: None
6
Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.r2b
Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.r2b
Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.r2b
Reading Atosiban_box_ctr.pdb...
Read 'GROningen MAchine for Chemical Simulation', 85 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 10 residues with 85 atoms

  chain  #res #atoms
  1 'A'    10     85

All occupancies are one
Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/atomtypes.atp
Atomtype 89Reading residue database... (amber14sb_parmbsc1)

Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/Merca.rtp
Residue 1
Sorting it all out...
Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/TYO.rtp
Residue 2
Sorting it all out...
Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.rtp
Residue 95
Sorting it all out...
Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.rtp
Residue 111
Sorting it all out...
Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.rtp
Residue 127
Sorting it all out...
Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.hdb
Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.hdb
Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.hdb
Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.n.tdb
Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.c.tdb

Back Off! I just backed up Atosiban_amber14sb.top to ./#Atosiban_amber14sb.top.6#
Processing chain 1 'A' (85 atoms, 10 residues)
Identified residue MER1 as a starting terminus.
Identified residue NH210 as a ending terminus.
1 out of 1 lines of specbond.dat converted successfully
Special Atom Distance matrix:
                    MER1
                     S11
    CYX6    SG63   0.200
Linking MER-1 S1-1 and CYX-6 SG-63...

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Program gmx pdb2gmx, VERSION 5.1.2
Source code file: /tmp/gromacs/5.1.2/iomkl-156233.188/gromacs-5.1.2/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1083

Fatal error:
There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Fix your terminal residues so that they match the residue database (.rtp) entries, or provide terminal database entries (.tdb).
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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Now indeed the MER and TYO as recognized as residues but I still obtain the dangling bond error

Thank you 

Stéphane