Priya Murugan

11 Questions 24 Answers 0 Followers

Questions related from Priya Murugan

Why the second reaction of my synthesis is not completing/working acc to TLC despite following a published method ?

Dear researchers, For the first rxn, I performed Claisen Schmidt condensation reaction to form an animated- diarylpentadienone product in cold conditions by dissolving aminoacetophenone in...

02 November 2023 2,918 5 View

How to split the huge ligand file from database into separate ligand files for molecular docking?

Hi researchers, I have downloaded 20,000 compounds from databases in .sdf format in a single file (size: 108 GB). Could someone guide me on splitting the enormous single ligand file into...

16 February 2023 6,049 9 View

Can 5-aminolevulinic acid hydrochloride be used instead of 5 - Aminolevulinic acid ?

Hi researchers, Can someone help clarify whether I can use 5-aminolevulinic acid hydrochloride (salt-form of aminolevulinic acid (ALA) instead of 5-aminolevulinic acid which is needed for the...

21 November 2022 1,615 2 View

How to recrystallize an oily compound after column chromatography ?

Hi researchers, I am currently synthesizing sulfonamide compounds by reacting aminoacetophenone with cinnamaldehyde using 6M NaOH (catalyst) and aqueous ethanol (solvent) at room temperature...

09 September 2022 4,624 7 View

Can anyone guide me on how to view the dssp secondary structure analysis generated by AMBER CPPTRAJ using gnuplot?

Hi researchers, I have used AMBER CPPTRAJ to generate dssp.gnu to view the 2D secondary structure of my protein throughout the molecular dynamic simulation using Gnuplot software....

19 May 2022 3,192 3 View

How to visualize the results generated from the analysis of MD trajectory using Cpptraj in AMBER16 ?

Hi researchers, I have used Amber16 to run a molecular dynamics simulation of my protein system for 50 ns. After the production run was completed, I have generated an MD trajectory with 2500...

24 March 2022 4,971 1 View

How to do shifting in residue numbering in Amber 16 to my topology files prmtop and rst7 ?

Hi, researchers, Kindly please guide me on how ambpdb from AmberTools which has the flag "-offset" can allow shifting in residue numbering? I tried but the amber doesn't recognise the flag...

09 June 2021 6,161 2 View

Which software or programme is suitable to be used to generate parameter for ligand that has Fe atom ?

Hi Researchers, I'm currently trying to generate parameters for the ligand and heme group that bind/crystallised with the protein structure. I need to know, which software or programme is the...

15 May 2021 3,176 8 View

How to choose the right files to be used as topology and coordinate file for amber ?

I have used ATB 3.0 software to generate parameters for my ligand and heme group molecules to prepare them for molecular dynamic simulation using Amber version 16 in Linux. However, I found there...

11 May 2021 8,103 2 View

Why I faced this error while using Antechamber in Amber 16 to generate parameters for my ligand that co-crystallized in protein ?

When I'm trying to use the antechamber in amber version 16, I couldn't proceed using it to generate parameters, topology and coordinate files as I got this type of error. The error mentioning...

11 May 2021 1,703 3 View

Does minimization require for average pdb structure extracted from 2drms plot using CPPTRAJ AMBER 16

Hi researcher, I'm really looking for your guidance and help in order for me to pursue my next step in computational work. I'm new to computational work and keen to learn more. Currently, I'm...

01 January 1970 6,885 2 View