25 Questions 36 Answers 0 Followers
Questions related from Rajiv Lakkaniga
I am trying to synthesize a compound which has both carboxylic acid and amine. During the purification, when I do the pH adjustment it forms a zwitterion and goes into the aqueous layer. Is there...
02 February 2020 6,807 3 View
In the body, when one develops a tumor, the microenvironment is very important. How do the cell cultures of cancer cells grow in the flasks without that micro-environment and only with the media...
02 February 2020 3,038 4 View
I am trying to grow cancer cells and do MTT assay for drug screening. Are there any alternatives to FBS? I know that FBS and FCS are widely used for cell culturing, but I am looking for other...
01 January 2020 4,795 4 View
Some proteins change their conformation based on protonation state of particular residues like aspartic acid. Some kinases are examples for this. For example, in case of Abl kinase, protonated...
11 November 2019 5,419 5 View
I am working on computationally understanding the active and inactive conformations of some proteins. Simulating the inactive conformation from the active conformation is reported in literature by...
10 October 2019 5,846 3 View
Is there a way to quantify (eg.: plots) the van der waal's or other hydrophobic interactions of a residue through a simulation? For example, using VMD, we can check for salt-bridges and hydrogen...
08 August 2019 816 3 View
I am trying to synthesize boronic acid pinacol ester derivatives from aryl/hetero-aryl halides. Is there any TLC staining technique which can indicate the formation of boronic acid? Thanks.
04 April 2019 583 10 View
Are there any bioisosteric replacements of triple bond (alkyne) which were employed for lead optimization or scaffold hopping? Thanks.
04 April 2019 2,805 5 View
I am doing an amide coupling reaction using HATU. The starting material is not very soluble in DMF. So, I am thinking of heating the reaction mixture to 65C. Is HATU stable at that temperature or...
09 September 2018 3,543 3 View
I am trying to do metadynamics simulation for my protein. Can someone explain what is a collective variable, and on what basis we decide collective variables in a metadynamics run? Thanks.
08 August 2018 5,739 4 View
I have performed a protein-ligand simulation in desmond. I would like to perform mmgbsa calculations on the trajectory. Can anyone help me with the proper syntax of the command. I tried...
06 June 2018 13,189 1 View
I am trying a coarse-grained simulation in gromacs to understand certain protein folding. I initially tried with triclinic box and -d 1.0. I used -c to center my protein in the solvent box. But...
05 May 2018 2,611 4 View
Hi, I did a MD simulation of a protein ligand complex using Desmond. I want to do the trajectory analysis and binding energy studies using gromacs tools. Is there a way to convert the desmond...
04 April 2018 8,716 1 View
I did a coarse grained simulation with martini parameters using Gromacs 5.0. Followed this: http://cgmartini.nl My simulation is done. But when I open the trajectory in VMD, I can see it only as...
04 April 2018 8,446 3 View
When the compound is formed as a salt in the reaction, can NMR be used to identify if the compound is de-salted? I mean, will the 'H' of HCl salt of my compound be identified by NMR? Thanks.
04 April 2018 6,617 15 View
Hi, I want to do an all-atom MD simulation without adding bias to a protein kinase. My starting conformation is DFG-in. How many nanoseconds of simulation is required, for the activation loop to...
03 March 2018 697 4 View
Hi, I am trying to run a MD simulation of a protein-ligand complex in a cluster. The npt run is complete and the log file doesn't show any error. Next the grompp also runs, without throwing any...
03 March 2018 5,444 5 View
I synthesized a molecule which has two chiral centers. So, I got diastereomers which I am able to separate through column. How do I determine the configuration of these molecules?
12 December 2017 4,781 14 View
I am trying to run an MD simulation in Desmond module of Schrodinger. I have it installed in Ububtu16.04. It looks to me that the run is taking too long. My CPU has 8 cores. How do I ensure that...
04 April 2017 2,360 3 View
hi, I have downloaded VMD1.9.3. i followed the installation procedures, changed paths etc. But when i enter 'vmd' command in the terminal, it thows an error. Please help me resolve this.
04 April 2017 9,371 4 View
I have been trying for 2 weeks now. It just doesn't work, although the conditions across the literature are pretty much the same. I tried to first make the isocyante from an aniline by dropwise...
03 March 2017 6,310 3 View
I synthesized a compound which could be either a cis or trans. How do I know determine which isomer was formed?
02 February 2017 4,477 5 View
I did a 10ns run for a protein-inhibitor complex and am currently doing analysis of the MD run. Can someone please explain what is B-factor value and it's significance in MD analysis. Also, what...
04 April 2016 1,159 1 View
Which journals are most suitable to publish results of protein molecular dynamics with enhanced sampling? The work is NOT new method developed, but studying a protein with existing techniques.
01 January 1970 9,968 5 View
Although biochemistry text books define pKa values for each residue, the actual pKa of a residue depends on several factors: location in the protein, presence of ions etc. So, given a protein...
01 January 1970 3,810 3 View
