Fayaz Ahmad

10 Questions 4 Answers 0 Followers

Questions related from Fayaz Ahmad

Question about pyred web server ?

hello i have a query is it anyone use the pyred server for amber ? i have query regardind

27 August 2024 1,341 0 View

Gromacs first step of minimization ?

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 3,599 1 View

Parametrize the residue (DOP) into the an .rtp entry but still did not recognize?

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 7,724 0 View

Residue 'DOP' not found in topology DATABASE ?

Hellow Does anyone have any idea how to solve this issue .. I am doing the MD simulation of phospholipids and glycolipids. Gromacs software show me this errors

01 May 2024 2,161 0 View

Equilibration did not reached for 5ns . nstlim is 5millions ?

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 2,084 0 View

Equilibration did not reached for 5ns . nstlim is 5millions ?

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 5,779 0 View

Amber20 to assign the solvateBox in xleap?

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 9,097 0 View

Amber20 step by step procedure ?

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 3,543 0 View

How to label and number atom for Md simulation?

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 2,836 0 View

How to label and number atom for Md simulation

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...

01 January 1970 6,317 6 View