Hello all. I have following error. please help I m new to gromacs

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question :-) GROMACS - gmx pdb2gmx, 2020.1-Ubuntu-2020.1-1 (-:

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Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
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and the project leaders:
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GROMACS: gmx pdb2gmx, version 2020.1-Ubuntu-2020.1-1
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/anand/Desktop/Kiranmd1
Command line:
gmx pdb2gmx -f 4jkv_clean.pdb -o 4jkv_processed.gro -water spce

Select the Force Field:
From current directory:
1: CHARMM all-atom force field
From ‘/usr/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 Charmm36-jul2022 force field in directory ./charmm36-jul2022.ff

going to rename ./charmm36-jul2022.ff/aminoacids.r2b
Opening force field file ./charmm36-jul2022.ff/aminoacids.r2b
going to rename ./charmm36-jul2022.ff/carb.r2b
Opening force field file ./charmm36-jul2022.ff/carb.r2b
going to rename ./charmm36-jul2022.ff/cgenff.r2b
Opening force field file ./charmm36-jul2022.ff/cgenff.r2b
going to rename ./charmm36-jul2022.ff/ethers.r2b
Opening force field file ./charmm36-jul2022.ff/ethers.r2b
going to rename ./charmm36-jul2022.ff/lipid.r2b
Opening force field file ./charmm36-jul2022.ff/lipid.r2b
going to rename ./charmm36-jul2022.ff/metals.r2b
Opening force field file ./charmm36-jul2022.ff/metals.r2b
going to rename ./charmm36-jul2022.ff/na.r2b
Opening force field file ./charmm36-jul2022.ff/na.r2b
going to rename ./charmm36-jul2022.ff/silicates.r2b
Opening force field file ./charmm36-jul2022.ff/silicates.r2b
going to rename ./charmm36-jul2022.ff/solvent.r2b
Opening force field file ./charmm36-jul2022.ff/solvent.r2b
Reading 4jkv_clean.pdb…
WARNING: all CONECT records are ignored
Read ‘SOLUBLE CYTOCHROME B562, SMOOTHENED HOMOLOG’, 3532 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 454 residues with 3532 atoms

chain #res #atoms
1 ‘A’ 454 3532

All occupancies are one
Opening force field file ./charmm36-jul2022.ff/atomtypes.atp
Reading residue database… (Charmm36-jul2022)
Opening force field file ./charmm36-jul2022.ff/aminoacids.rtp
Opening force field file ./charmm36-jul2022.ff/carb.rtp
Opening force field file ./charmm36-jul2022.ff/cgenff.rtp
Opening force field file ./charmm36-jul2022.ff/ethers.rtp
Opening force field file ./charmm36-jul2022.ff/lipid.rtp
Opening force field file ./charmm36-jul2022.ff/metals.rtp
Opening force field file ./charmm36-jul2022.ff/na.rtp
Opening force field file ./charmm36-jul2022.ff/silicates.rtp
Opening force field file ./charmm36-jul2022.ff/solvent.rtp
Opening force field file ./charmm36-jul2022.ff/aminoacids.hdb
Opening force field file ./charmm36-jul2022.ff/carb.hdb
Opening force field file ./charmm36-jul2022.ff/cgenff.hdb
Opening force field file ./charmm36-jul2022.ff/ethers.hdb
Opening force field file ./charmm36-jul2022.ff/lipid.hdb
Opening force field file ./charmm36-jul2022.ff/metals.hdb
Opening force field file ./charmm36-jul2022.ff/na.hdb
Opening force field file ./charmm36-jul2022.ff/silicates.hdb
Opening force field file ./charmm36-jul2022.ff/solvent.hdb
Opening force field file ./charmm36-jul2022.ff/aminoacids.n.tdb
Opening force field file ./charmm36-jul2022.ff/carb.n.tdb
Opening force field file ./charmm36-jul2022.ff/cgenff.n.tdb
Opening force field file ./charmm36-jul2022.ff/ethers.n.tdb
Opening force field file ./charmm36-jul2022.ff/lipid.n.tdb
Opening force field file ./charmm36-jul2022.ff/metals.n.tdb
Opening force field file ./charmm36-jul2022.ff/na.n.tdb
Opening force field file ./charmm36-jul2022.ff/silicates.n.tdb
Opening force field file ./charmm36-jul2022.ff/solvent.n.tdb
Opening force field file ./charmm36-jul2022.ff/aminoacids.c.tdb
Opening force field file ./charmm36-jul2022.ff/carb.c.tdb
Opening force field file ./charmm36-jul2022.ff/cgenff.c.tdb
Opening force field file ./charmm36-jul2022.ff/ethers.c.tdb
Opening force field file ./charmm36-jul2022.ff/lipid.c.tdb
Opening force field file ./charmm36-jul2022.ff/metals.c.tdb
Opening force field file ./charmm36-jul2022.ff/na.c.tdb
Opening force field file ./charmm36-jul2022.ff/silicates.c.tdb
Opening force field file ./charmm36-jul2022.ff/solvent.c.tdb
Processing chain 1 ‘A’ (3532 atoms, 454 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 646 donors and 635 acceptors were found.
There are 842 hydrogen bonds
Will use HISE for residue 63
Will use HISH for residue 227
Will use HISE for residue 231
Will use HISE for residue 340
Will use HISE for residue 361
Will use HISE for residue 433
Will use HISE for residue 470
Identified residue GLY-1 as a starting terminus.
Identified residue CYS550 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET33 MET58 HIS63 CYS193 CYS213 CYS217 HIS227
SD262 SD447 NE2497 SG855 SG1014 SG1041 NE21124
MET58 SD447 2.190
HIS63 NE2497 1.890 1.460
CYS193 SG855 1.995 1.990 2.165
CYS213 SG1014 2.167 2.163 2.341 0.204
CYS217 SG1041 2.376 2.255 1.466 1.571 1.641
HIS227 NE21124 2.954 2.148 1.588 1.963 2.024 0.826
MET230 SD1148 3.821 2.963 2.255 2.914 2.953 1.599 0.982
HIS231 NE21159 3.104 2.437 1.562 2.418 2.492 1.009 0.566
CYS244 SG1247 5.001 4.500 3.401 4.611 4.666 3.071 2.760
CYS273 SG1479 4.907 4.892 3.764 4.302 4.301 2.855 2.856
MET286 SD1584 3.119 3.312 1.927 3.196 3.290 1.708 1.940
CYS295 SG1648 2.257 2.250 1.347 1.645 1.730 0.203 0.948
MET301 SD1690 2.803 2.514 2.035 1.474 1.465 0.658 0.910
CYS314 SG1787 2.966 3.219 2.262 2.233 2.242 0.967 1.491
MET326 SD1887 4.717 4.614 3.717 3.718 3.674 2.497 2.495
HIS340 NE22006 7.100 6.805 5.903 6.099 6.047 4.856 4.667
HIS361 NE22153 5.720 5.906 4.715 5.219 5.209 3.820 3.898
CYS390 SG2362 3.005 3.136 2.165 2.268 2.285 0.894 1.334
MET424 SD2632 7.360 6.857 6.092 6.200 6.138 5.037 4.746
HIS433 NE22706 8.286 7.967 6.990 7.433 7.395 6.095 5.874
MET449 SD2817 6.930 6.613 5.585 6.192 6.177 4.775 4.556
CYS469 SG2975 4.813 3.980 3.399 3.603 3.581 2.454 1.940
HIS470 NE22985 4.529 4.053 3.303 3.400 3.369 2.171 1.908
CYS490 SG3172 3.440 2.390 2.952 1.561 1.482 2.247 2.055
CYS507 SG3197 3.621 2.499 3.057 1.751 1.671 2.338 2.085
MET525 SD3339 4.462 4.053 3.086 3.672 3.683 2.219 1.976
MET532 SD3386 5.627 5.201 4.201 4.893 4.896 3.441 3.169
CYS550 SG3532 5.990 6.128 4.758 6.280 6.363 4.744 4.746
MET230 HIS231 CYS244 CYS273 MET286 CYS295 MET301
SD1148 NE21159 SG1247 SG1479 SD1584 SG1648 SD1690
HIS231 NE21159 0.733
CYS244 SG1247 1.923 2.250
CYS273 SG1479 2.240 2.487 1.635
MET286 SD1584 1.892 1.475 2.025 2.100
CYS295 SG1648 1.682 1.043 3.054 2.863 1.575
MET301 SD1690 1.619 1.285 3.276 2.895 2.214 0.854
CYS314 SG1787 1.780 1.442 2.819 2.135 1.547 0.983 1.066
MET326 SD1887 2.033 2.328 2.338 1.073 2.459 2.572 2.302
HIS340 NE22006 3.890 4.420 3.185 2.350 4.417 4.926 4.658
HIS361 NE22153 3.294 3.527 2.337 1.058 2.912 3.813 3.858
CYS390 SG2362 1.582 1.249 2.652 2.063 1.439 0.915 1.024
MET424 SD2632 3.946 4.554 3.447 2.816 4.782 5.132 4.772
HIS433 NE22706 5.015 5.555 3.872 3.395 5.390 6.144 5.971
MET449 SD2817 3.690 4.191 2.455 2.075 3.981 4.809 4.725
CYS469 SG2975 1.175 1.848 2.109 2.038 2.738 2.579 2.204
HIS470 NE22985 1.312 1.780 2.096 1.502 2.375 2.279 1.935
CYS490 SG3172 2.763 2.619 4.679 4.506 3.892 2.418 1.810
CYS507 SG3197 2.734 2.643 4.652 4.496 3.954 2.515 1.881
MET525 SD3339 1.214 1.622 1.332 1.060 1.843 2.264 2.222
MET532 SD3386 2.290 2.787 1.264 1.129 2.740 3.476 3.432
CYS550 SG3532 4.158 4.188 2.444 3.002 3.092 4.640 5.131
CYS314 MET326 HIS340 HIS361 CYS390 MET424 HIS433
SG1787 SD1887 NE22006 NE22153 SG2362 SD2632 NE22706
MET326 SD1887 1.756
HIS340 NE22006 4.164 2.432
HIS361 NE22153 3.003 1.817 2.045
CYS390 SG2362 0.206 1.716 4.107 2.974
MET424 SD2632 4.442 2.713 0.776 2.724 4.369
HIS433 NE22706 5.420 3.760 1.442 2.842 5.350 1.701
MET449 SD2817 4.147 2.621 1.156 1.742 4.057 1.633 1.436
CYS469 SG2975 2.295 1.571 2.978 2.970 2.144 2.900 4.178
HIS470 NE22985 1.748 0.861 2.788 2.447 1.630 2.878 4.076
CYS490 SG3172 2.866 3.749 5.841 5.483 2.832 5.744 7.187
CYS507 SG3197 2.935 3.728 5.766 5.476 2.892 5.645 7.107
MET525 SD3339 1.800 1.138 2.828 2.097 1.648 3.041 3.943
MET532 SD3386 2.937 1.681 1.935 1.629 2.811 2.217 2.806
CYS550 SG3532 4.338 4.057 4.378 2.902 4.243 4.919 4.490
MET449 CYS469 HIS470 CYS490 CYS507 MET525 MET532
SD2817 SG2975 NE22985 SG3172 SG3197 SD3339 SD3386
CYS469 SG2975 3.015
HIS470 NE22985 2.877 0.750
CYS490 SG3172 6.056 3.126 3.199
CYS507 SG3197 5.993 3.042 3.153 0.203
MET525 SD3339 2.593 1.140 0.807 3.674 3.647
MET532 SD3386 1.415 1.799 1.676 4.791 4.739 1.228
CYS550 SG3532 3.365 4.463 4.223 6.776 6.792 3.445 3.065

Linking CYS-193 SG-855 and CYS-213 SG-1014…
Linking CYS-217 SG-1041 and CYS-295 SG-1648…
Linking CYS-314 SG-1787 and CYS-390 SG-2362…
Linking CYS-490 SG-3172 and CYS-507 SG-3197…
Start terminus GLY–1: GLY-NH3+
End terminus CYS-550: COO-
Opening force field file ./charmm36-jul2022.ff/aminoacids.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.

Program: gmx pdb2gmx, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 130)

Fatal error:
Residue 7 named ASP of a molecule in the input file was mapped
to an entry in the topology database, but the atom CG used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

2

atom should be fixed，u can try swiss-pdb viewer software

3

The error is saying your pdb file has atoms missing from the aspartic acid residue. You can search up tools online for fixing pdb files, such as this automated server for repairing protein pdb files (https://pubs.acs.org/doi/10.1021/acs.jcim.2c00571)

4

search with this in google, you will find a lot of hits.

5

Thanks Error fixed.

6

Thanks error fixed.

7

anand@anand:~/Downloads/12/gromacs-2024.1/build$ cmake … -DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
– The C compiler identification is GNU 9.4.0
– The CXX compiler identification is GNU 9.4.0
– Detecting C compiler ABI info
– Detecting C compiler ABI info - done
– Check for working C compiler: /usr/bin/cc - skipped
– Detecting C compile features
– Detecting C compile features - done
– Detecting CXX compiler ABI info
– Detecting CXX compiler ABI info - done
– Check for working CXX compiler: /usr/bin/c++ - skipped
– Detecting CXX compile features
– Detecting CXX compile features - done
– Found Python3: /usr/bin/python3.8 (found suitable version “3.8.10”, minimum required is “3.7”) found components: Interpreter Development Development.Module Development.Embed
– Selected GPU FFT library - cuFFT
– Found OpenMP_C: -fopenmp (found version “4.5”)
– Found OpenMP_CXX: -fopenmp (found version “4.5”)
– Found OpenMP: TRUE (found version “4.5”)
– Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
– Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
– Performing Test CFLAGS_EXCESS_PREC
– Performing Test CFLAGS_EXCESS_PREC - Success
– Performing Test CFLAGS_COPT
– Performing Test CFLAGS_COPT - Success
– Performing Test CFLAGS_NOINLINE
– Performing Test CFLAGS_NOINLINE - Success
– Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
– Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
– Performing Test CXXFLAGS_EXCESS_PREC
– Performing Test CXXFLAGS_EXCESS_PREC - Success
– Performing Test CXXFLAGS_COPT
– Performing Test CXXFLAGS_COPT - Success
– Performing Test CXXFLAGS_NOINLINE
– Performing Test CXXFLAGS_NOINLINE - Success
– Looking for include file unistd.h
– Looking for include file unistd.h - found
– Looking for include file pwd.h
– Looking for include file pwd.h - found
– Looking for include file dirent.h
– Looking for include file dirent.h - found
– Looking for include file time.h
– Looking for include file time.h - found
– Looking for include file sys/time.h
– Looking for include file sys/time.h - found
– Looking for include file io.h
– Looking for include file io.h - not found
– Looking for include file sched.h
– Looking for include file sched.h - found
– Looking for include file xmmintrin.h
– Looking for include file xmmintrin.h - found
– Looking for gettimeofday
– Looking for gettimeofday - found
– Looking for sysconf
– Looking for sysconf - found
– Looking for nice
– Looking for nice - found
– Looking for fsync
– Looking for fsync - found
– Looking for _fileno
– Looking for _fileno - not found
– Looking for fileno
– Looking for fileno - found
– Looking for _commit
– Looking for _commit - not found
– Looking for sigaction
– Looking for sigaction - found
– Performing Test HAVE_BUILTIN_CLZ
– Performing Test HAVE_BUILTIN_CLZ - Success
– Performing Test HAVE_BUILTIN_CLZLL
– Performing Test HAVE_BUILTIN_CLZLL - Success
– Looking for clock_gettime in rt
– Looking for clock_gettime in rt - found
– Looking for feenableexcept in m
– Looking for feenableexcept in m - found
– Looking for fedisableexcept in m
– Looking for fedisableexcept in m - found
– Checking for sched.h GNU affinity API
– Performing Test sched_affinity_compile
– Performing Test sched_affinity_compile - Success
– Looking for include file mm_malloc.h
– Looking for include file mm_malloc.h - found
– Looking for include file malloc.h
– Looking for include file malloc.h - found
– Checking for _mm_malloc()
– Checking for _mm_malloc() - supported
– Looking for posix_memalign
– Looking for posix_memalign - found
– Looking for memalign
– Looking for memalign - not found
– Using default binary suffix: “”
– Using default library suffix: “”
– Performing Test CMAKE_HAVE_LIBC_PTHREAD
– Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
– Looking for pthread_create in pthreads
– Looking for pthread_create in pthreads - not found
– Looking for pthread_create in pthread
– Looking for pthread_create in pthread - found
– Found Threads: TRUE
– Looking for C++ include pthread.h
– Looking for C++ include pthread.h - found
– Performing Test TEST_ATOMICS
– Performing Test TEST_ATOMICS - Success
– Atomic operations found
– Performing Test PTHREAD_SETAFFINITY
– Performing Test PTHREAD_SETAFFINITY - Success
– Detecting best SIMD instructions for this CPU
– Checking for GCC x86 inline asm
– Checking for GCC x86 inline asm - supported
– Detected build CPU features - aes apic avx clfsh cmov cx8 cx16 htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt
– Detected build CPU brand - Intel(R) Core™ i5-2320 CPU @ 3.00GHz
– Detected best SIMD instructions for this CPU - AVX_256
– Performing Test C_mavx_FLAG_ACCEPTED
– Performing Test C_mavx_FLAG_ACCEPTED - Success
– Performing Test C_mavx_COMPILE_WORKS
– Performing Test C_mavx_COMPILE_WORKS - Success
– Performing Test CXX_mavx_FLAG_ACCEPTED
– Performing Test CXX_mavx_FLAG_ACCEPTED - Success
– Performing Test CXX_mavx_COMPILE_WORKS
– Performing Test CXX_mavx_COMPILE_WORKS - Success
– Enabling 256-bit AVX SIMD instructions using CXX flags: -mavx
– Detecting flags to enable runtime detection of AVX-512 units on newer CPUs
– Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED
– Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed
– Performing Test C_xCORE_AVX512_FLAG_ACCEPTED
– Performing Test C_xCORE_AVX512_FLAG_ACCEPTED - Failed
– Performing Test C_mavx512f_mfma_mavx512vl_mavx512dq_mavx512bw_FLAG_ACCEPTED
– Performing Test C_mavx512f_mfma_mavx512vl_mavx512dq_mavx512bw_FLAG_ACCEPTED - Success
– Performing Test C_mavx512f_mfma_mavx512vl_mavx512dq_mavx512bw_COMPILE_WORKS
– Performing Test C_mavx512f_mfma_mavx512vl_mavx512dq_mavx512bw_COMPILE_WORKS - Success
– Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED
– Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed
– Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED
– Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED - Failed
– Performing Test CXX_mavx512f_mfma_mavx512vl_mavx512dq_mavx512bw_FLAG_ACCEPTED
– Performing Test CXX_mavx512f_mfma_mavx512vl_mavx512dq_mavx512bw_FLAG_ACCEPTED - Success
– Performing Test CXX_mavx512f_mfma_mavx512vl_mavx512dq_mavx512bw_COMPILE_WORKS
– Performing Test CXX_mavx512f_mfma_mavx512vl_mavx512dq_mavx512bw_COMPILE_WORKS - Success
– Detecting flags to enable runtime detection of AVX-512 units on newer CPUs - -mavx512f -mfma -mavx512vl -mavx512dq -mavx512bw
– Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED
– Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED - Success
– Performing Test _callconv___vectorcall
– Performing Test _callconv___vectorcall - Failed
– Performing Test _callconv___regcall
– Performing Test _callconv___regcall - Failed
– Performing Test callconv
– Performing Test callconv - Success
– Found CUDA: /usr/local/cuda (found suitable version “12.4”, minimum required is “11.0”)
– Adding work-around for issue compiling CUDA code with glibc 2.23 string.h
– Check for working NVCC/C++ compiler combination with nvcc ‘/usr/local/cuda/bin/nvcc’
– Check for working NVCC/C++ compiler combination - works
– Checking if nvcc accepts flags --generate-code=arch=compute_35,code=sm_35
– Checking if nvcc accepts flags --generate-code=arch=compute_35,code=sm_35 - No
– Checking if nvcc accepts flags --generate-code=arch=compute_37,code=sm_37
– Checking if nvcc accepts flags --generate-code=arch=compute_37,code=sm_37 - No
– Checking if nvcc accepts flags --generate-code=arch=compute_50,code=sm_50
– Checking if nvcc accepts flags --generate-code=arch=compute_50,code=sm_50 - Yes
– Checking if nvcc accepts flags --generate-code=arch=compute_52,code=sm_52
– Checking if nvcc accepts flags --generate-code=arch=compute_52,code=sm_52 - Yes
– Checking if nvcc accepts flags --generate-code=arch=compute_60,code=sm_60
– Checking if nvcc accepts flags --generate-code=arch=compute_60,code=sm_60 - Yes
– Checking if nvcc accepts flags --generate-code=arch=compute_61,code=sm_61
– Checking if nvcc accepts flags --generate-code=arch=compute_61,code=sm_61 - Yes
– Checking if nvcc accepts flags --generate-code=arch=compute_70,code=sm_70
– Checking if nvcc accepts flags --generate-code=arch=compute_70,code=sm_70 - Yes
– Checking if nvcc accepts flags --generate-code=arch=compute_75,code=sm_75
– Checking if nvcc accepts flags --generate-code=arch=compute_75,code=sm_75 - Yes
– Checking if nvcc accepts flags --generate-code=arch=compute_80,code=sm_80
– Checking if nvcc accepts flags --generate-code=arch=compute_80,code=sm_80 - Yes
– Checking if nvcc accepts flags --generate-code=arch=compute_86,code=sm_86
– Checking if nvcc accepts flags --generate-code=arch=compute_86,code=sm_86 - Yes
– Checking if nvcc accepts flags --generate-code=arch=compute_89,code=sm_89
– Checking if nvcc accepts flags --generate-code=arch=compute_89,code=sm_89 - Yes
– Checking if nvcc accepts flags --generate-code=arch=compute_90,code=sm_90
– Checking if nvcc accepts flags --generate-code=arch=compute_90,code=sm_90 - Yes
– Checking if nvcc accepts flags -Wno-deprecated-gpu-targets
– Checking if nvcc accepts flags -Wno-deprecated-gpu-targets - Yes
– Checking if nvcc accepts flags --generate-code=arch=compute_53,code=sm_53
– Checking if nvcc accepts flags --generate-code=arch=compute_53,code=sm_53 - Yes
– Checking if nvcc accepts flags --generate-code=arch=compute_80,code=sm_80
– Checking if nvcc accepts flags --generate-code=arch=compute_80,code=sm_80 - Yes
– Checking if nvcc accepts flags -use_fast_math
– Checking if nvcc accepts flags -use_fast_math - Yes
– Checking if nvcc accepts flags -Xptxas;-warn-double-usage
– Checking if nvcc accepts flags -Xptxas;-warn-double-usage - Yes
– Checking if nvcc accepts flags -Xptxas;-Werror
– Checking if nvcc accepts flags -Xptxas;-Werror - Yes
– The CUDA compiler identification is unknown
CMake Error at /usr/local/share/cmake-3.28/Modules/CMakeDetermineCUDACompiler.cmake:270 (message):
Failed to detect a default CUDA architecture.

Compiler output:

Call Stack (most recent call first):
cmake/gmxManageCuda.cmake:116 (enable_language)
CMakeLists.txt:699 (include)

– Configuring incomplete, errors occurred!