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Questions related from Suraj Pukhrambam
I have read some papers but i didn't get proper answers. In some cases, my level of theory is not exactly written. I will be very gladfull for any recommendation
11 June 2024 9,877 1 View
I have intel iris xe graphic card. i want to run dft calculation in gaussian using a gpu. what are the necessary modifications to the input file? my input file read like...
22 May 2024 3,340 6 View
while trying to generate CGenFF topology for Ligand after extracting from docked file, i got error which i'm showing as a picture. What could be the possible reason and how will i rectify it for...
27 March 2024 2,379 3 View
While trying to run MD simulation for 50ns, i got some errors read as "WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 500000 WRITING COORDINATES TO DCD FILE output.dcd AT STEP 500000 WRITING...
10 January 2024 7,458 8 View
I'm trying to perform MD simulation of protein-ligand complex. The step5_production.inp was set for 100ns. After running for around 30ns the program stop automatically. How will i modify the file...
07 January 2024 1,476 1 View
The RMSD trajectory for bare protein nd complex almost identical. So when i plot it i cannot diffrentiate it.
17 November 2023 7,546 2 View
To study the vibrational spectroscopy
10 November 2023 8,125 3 View
While using charmm-gui, there seems to be some error which i have no answer
06 October 2023 9,693 2 View
After uploading ligand-protein docked pdb structure and PDB manipulation options, when i click Next step: Generate PDB, it always shows CHARMM was terminated abnormally. Any recommendation how to...
09 September 2023 5,323 3 View
I have been working MD simulation in windows using NAMD and Charm GUI but it take lots of time to run even for 10ns. I have a workstation having 64gb RAM, 8 core and 16 process with graphic card....
28 August 2023 6,238 1 View
My ligand is a metal complex conatining Ag (Silver). So when i tried to run Molecular docking using Autodock vina as well as PyRx, it shows error as "Parse error on line 15 in file...
01 January 1970 3,894 3 View
I have been performing Molecular Dynamic simulation. While calculating RMSD trajectory for protein and protein + Ligand, there is sudden increase in the trajectory tools. What could be possible...
01 January 1970 9,861 3 View
