Hello, I have paramterize the residue namely “DOP” into both files of amino acids.rtp and lipids.rtp files of GROMOS96 53a6 force field and charmm27… respectively, although I mentioned the residue name in residuetypes.dat and follow the same syntax but still my gromacs did not catch the residue. Does anyone know how to fix this problem? below is the error. Using the Charmm27 force field in directory charmm27.ff
going to rename charmm27.ff/aminoacids.r2b Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.r2b
going to rename charmm27.ff/rna.r2b Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.r2b Reading dopcglu.pdb… WARNING: all CONECT records are ignored Read ‘Built with Packmol’, 9600 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 300 residues with 9600 atoms
chain #res #atoms
1 ‘C’ 75 2550
2 ‘D’ 75 2250
3 ‘E’ 75 2550
4 ‘F’ 75 2250
All occupancies are one All occupancies are one Opening force field file /usr/share/gromacs/top/charmm27.ff/atomtypes.atp
Reading residue database… (Charmm27) Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.rtp Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.rtp Opening force field file /usr/share/gromacs/top/charmm27.ff/lipids.rtp Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.rtp 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.7#
Processing chain 1 ‘C’ (2550 atoms, 75 residues)
Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully
Program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2 Source file: src/gromacs/gmxpreprocess/resall.cpp (line 597)
Fatal error: Residue ‘DOP’ not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
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