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Questions related from Suraj Pukhrambam
I have performed molecular docking of multiple ligands against a target receptor. I want to perform MD simulation of the protein ligands complex using CHARMM-GUI and NAMD2. How will I generate...
4 weeks ago 8,821 3 View
I want to analyst vibrational assignment with PED calculation with the help of Molvib package. They have provided an executable rdarch.exe for converting Gaussian log file to .dat file, which is...
29 April 2025 6,810 0 View
After creating .dd2 file, I couldn't go further to calculate and optimize to obtain {file_name.dd2}. Any recommendation to solve it.
05 February 2025 5,202 0 View
While dokcing metal complex containing Ag, i have modified the force fiel parameters to include the Ag. But still Autodock4.2.6 shows error. I have also attached the error as well as the modified...
01 July 2024 9,334 0 View
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 9,972 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 3,462 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 2,557 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 7,510 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 1,570 1 View
I,m trying to analyse vibrational assignments of compound containing 122 atoms .fmu files is put in the VEDA. After this while clicking the Calculate button, after some calculatios it stops and i...
02 December 2023 9,453 1 View
The RMSD trajectory for bare protein nd complex almost identical. So when i plot it i cannot diffrentiate it.
17 November 2023 7,594 2 View
To study the vibrational spectroscopy
10 November 2023 8,181 3 View
While using charmm-gui, there seems to be some error which i have no answer
06 October 2023 9,765 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 5,372 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 6,316 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 3,941 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 9,914 3 View
