I'm looking to calculate charges for my ligand and later run MD simulation on them. I ran into this error suddenly when it had worked in the past. I have Gaussian 16 installed.
My slurm.out
Net charge: -1
Net charge: -1
Charge and Multiplicity [0,1]? Percent or Route card? Percent or Route card? Percent or Route card? Percent or Route card? Route card? Titles? Titles? Charge and Multiplicity? ../../simulation_OTP111_3One_0_Emin.sh: line 25: /programs/g16: Is a directory
Error termination in NtrErr:
ntran open failure returned to fopen.
Error: segmentation violation
rax 0000000000000000, rbx 0000000005c10e60, rcx ffffffffffffffff
rdx 0000000000038f42, rsp 00007fffffa34778, rbp 00007fffffa347b0
rsi 000000000000000b, rdi 0000000000038f42, r8 00002aaaaaae8800
r9 00002aaaaaae8800, r10 00007fffffa33b60, r11 0000000000000206
r12 0000000000000000, r13 0000000005c04598, r14 00007fffffa39bd0
r15 00007fffffa39910
/lib64/libpthread.so.0(+0xf630) [0x2aaaab0ab630]
/lib64/libc.so.6(kill+0x7) [0x2aaaab5f0657]
/programs/g16/newzmat() [0x458fc5]
/programs/g16/newzmat() [0x49ccb9]
/programs/g16/newzmat() [0x4873f2]
/programs/g16/newzmat() [0x434284]
/programs/g16/newzmat() [0x411a36]
/programs/g16/newzmat() [0x4109a6]
/programs/g16/newzmat() [0x410864]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2aaaab5dc555]
/programs/g16/newzmat() [0x40afa9]
/scratch1/alex/glyco_project/glycomimetics/scripts/make_gaussian_input_file.sh: line 52: 233282 Aborted /programs/g16/newzmat -ichk -ozmat -prompt ${old_chk} ${gaussian_input} < newzmat_here_esp.txt
../../simulation_OTP111_3One_0_Emin.sh: line 31: /programs/g16: Is a directory
Num atoms : 19
Getting ESP charges on OTP111_3One_0_ligand_esp_g16.log
Running Resp
Error: No ESP fitting centers and fitting values exist, adding 'iop(6/33=2) iop(6/42=6)' to the key word list
/scratch1/alex/glyco_project/glycomimetics/scripts/Run.resp: line 42: /scratch2/alex/Set5/Trial_1/simulation/analog_OTP111_3One_0/1_leap/resp-2.2/resp: No such file or directory
Slurm script ends
Few troubleshooting steps:
1. Check the input file: Ensure that your Gaussian input file is properly formatted and contains all the necessary information. Verify that you have specified the correct molecular structure, basis set, and other relevant parameters.
2. Check the Gaussian software installation: Make sure that Gaussian 16 is correctly installed on your system and that the installation is not corrupted. You can try running a simple test calculation to confirm that Gaussian 16 is functioning properly.
3. Check the Gaussian license: If you are using a licensed version of Gaussian, verify that your license is up to date and valid. In case of any issues with the license, contact the Gaussian support team for assistance.
4. Check the system resources: Ensure that your computer has sufficient resources to perform the calculations. Insufficient memory or disk space can sometimes lead to errors during Gaussian calculations. Check the available memory and disk space on your system and consider freeing up resources if necessary.
5. Check the error message: Examine the specific error message or output generated by Gaussian. It may provide clues about the nature of the problem and help identify potential solutions. If you're unsure about the error message, you can search the Gaussian documentation or seek assistance from the Gaussian user community.
6. Update Gaussian: If you have been using an older version of Gaussian 16, consider updating to the latest version. Newer versions often include bug fixes and improvements that can resolve issues encountered in previous versions.
Hope it helps:credit AI
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