pdb2gmx error
Summary
When running the latest version of pdb2gmx, file output is not correct when using oplsaam.ff. A little old, but working fine when using 2020.6
GROMACS version
:-) GROMACS - gmx_mpi, 2022.1 (-:
Command line:
gmx_mpi -quiet --version
GROMACS version: 2022.1
Precision: mixed
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128)
GPU support: CUDA
SIMD instructions: AVX2_256
CPU FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128
GPU FFT library: cuFFT
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
C compiler: /usr/bin/cc GNU 7.5.0
C compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG
C++ compiler: /usr/bin/c++ GNU 7.5.0
C++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG
CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2021 NVIDIA Corporation;Built on Mon_Sep_13_19:13:29_PDT_2021;Cuda compilation tools, release 11.5, V11.5.50;Build cuda_11.5.r11.5/compiler.30411180_0
CUDA compiler flags:-std=c++14;;-D_FORCE_INLINES;-mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG
CUDA driver: 11.50
CUDA runtime: 11.50
Steps to reproduce
gmx_mpi pdb2gmx -f ../receptor_data/5q17_processed.pdb
What is the current bug behavior?
:-) GROMACS - gmx pdb2gmx, 2022.1 (-:
Command line:
gmx_mpi pdb2gmx -f ../receptor_data/5q17_processed.pdb
Select the Force Field:
From current directory:
1: OPLS-AA/M all-atom force field (2015 aminoacid dihedrals)
From '/home/gromacs-2022.1/share/gromacs/top':
2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
10: GROMOS96 43a1 force field
11: GROMOS96 43a2 force field (improved alkane dihedrals)
12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
1
Using the Oplsaam force field in directory ./oplsaam.ff
Opening force field file ./oplsaam.ff/watermodels.dat
Select the Water Model:
1: TIP4P TIP 4-point, recommended
2: TIP3P TIP 3-point
3: TIP5P TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
4: TIP5P TIP 5-point improved for Ewald sums
5: SPC simple point charge
6: SPC/E extended simple point charge
7: None
1
going to rename ./oplsaam.ff/aminoacids.r2b
Opening force field file ./oplsaam.ff/aminoacids.r2b
Reading ../receptor_data/5q17_processed.pdb...
Read '', 3871 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 2 chains and 0 blocks of water and 236 residues with 3871 atoms
chain #res #atoms
1 ' ' 224 3662
2 ' ' 12 209
there were 2106 atoms with zero occupancy and 1765 atoms with occupancy unequal to one (out of 3871 atoms). Check your pdb file.
there were 2106 atoms with zero occupancy and 1765 atoms with occupancy unequal to one (out of 3871 atoms). Check your pdb file.
Opening force field file ./oplsaam.ff/atomtypes.atp
Reading residue database... (Oplsaam)
Opening force field file ./oplsaam.ff/aminoacids.rtp
Opening force field file ./oplsaam.ff/aminoacids.hdb
Opening force field file ./oplsaam.ff/aminoacids.n.tdb
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Program: gmx pdb2gmx, version 2022.1
Source file: src/gromacs/gmxpreprocess/ter_db.cpp (line 139)
Function: void read_atom(char*, bool, std::__cxx11::string*, t_atom*, PreprocessingAtomTypes*, int*)
Inconsistency in user input:
Atomtype for atom name oplsm_298 not found in terminal data base
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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Please find attached the file for your review.tmp.tar.gz
Edited by Andrey Alekseenko