Saikat Pal

Installation problem

16

I am getting the following error: ERROR: cannot verify victor.poshtiban.io's certificate, issued by ‘CN=R3,O=Let's Encrypt,C=US’: Issued certificate has expired. To connect to victor.poshtiban.io insecurely, use `--no-check-certificate'. error: sorry something went...

installation problem

1

saikat@saikat-ROG-Strix:~/Downloads/fl2000_drm-master$ make make CHECK="/usr/bin/sparse" -C /lib/modules/5.13.0-28-generic/build M=/home/saikat/Downloads/fl2000_drm-master modules make[1]: Entering directory '/usr/src/linux-headers-5.13.0-28-generic' CC [M] /home/saikat/Downloads/fl2000_drm-master/fl2000_gem.o /home/saikat/Downloads/fl2000_drm-master/fl2000_gem.c: In function ‘fl2000_gem_prime_import_sg_table’: /home/saikat/Downloads/fl2000_drm-master/fl2000_gem.c:234:8: error: implicit declaration of function ‘drm_prime_sg_to_page_addr_arrays’; did you mean ‘drm_prime_sg_to_dma_addr_array’?...

I have installed CUDA version OpenMM8.1 on HPC. However, I am getting an error: "/var/lib/slurm/slurmd/job34223357/slurm_script: line 24: 36322 Bus error python openmm_input.py > outfile". Although, I ran the same input...

I am trying to run pyautofep using the [tutorial.](https://github.com/luancarvalhomartins/PyAutoFEP/tree/master/docs/tutorial01) However, I am getting the following error : =================== STACK INFO =================== File "/home/saikat/saikat/pyautofep/test-saikat/prepare_dual_topology.py", line 3825, in arguments = process_user_input.read_options(Parser, unpack_section='prepare_dual_topology')...

I am trying to run the tutorial (https://github.com/UCL-CCS/TIES_MD/tree/main/TIES_MD/examples/NAMD/ethane_namd/zero_sum/leg1) using the same prmtop and pdb files. However, I am getting the following error: Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA...

problem regarding "change" command in cpptraj

3

Dear all, I have converted my topology file with added PDB information (like chain ID and renumbering PDB) using "parmed". However, the previously mentioned information still missing in output file...

DNA elasticity

1

I want to calculate DNA elasticity using CPPTRAJ. This is compatible in gromacs https://do-x3dna.readthedocs.io/en/latest/about_dna_elasticity.html Is It possible to calculate DNA elasticity using CPPTRAJ