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Questions related from Fayaz Ahmad
I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...
08 August 2024 2,459 1 View
Hello, I have paramterize the residue namely “DOP” into both files of amino acids.rtp and lipids.rtp files of GROMOS96 53a6 force field and charmm27… respectively, although I mentioned the residue...
20 June 2024 7,529 0 View
Hi everyone I try to perform equilibration on my system in AMBER16. I use pmemd.cuda and follow AMBER tutorials. This step is interrupted during execution and remains incomplete. also I have the...
22 March 2024 1,882 0 View
Hi, I have a question I am doing the equilibration but here the problem is that when nstep reaches up to 4 lac, and the simulation cancels. below is the script molecular dynamics run &cntrl...
08 March 2024 5,620 0 View
Hello, I am using the amber software to perform the MD Simulation of both glyco and phospho lipids while using the amber software here in the xleap I face the issue when I use the script...
07 December 2023 9,025 0 View
How I can used AmberTools 20 (all steps) to make Molecular Dynamics Simulations for carbohydrates and lipids like i have a mixture of both glycolipids and phopholipids.
07 September 2023 3,483 0 View
Hellow Everyone . I have a query that i have build a monomer of both phospholipids and glycolipids for Md Simulation but the problem which i face is that once i go to tool/software and put the...
07 August 2023 2,778 0 View
01 January 1970 6,267 6 View
