How to use the NAMD output file for molecular docking?

I optimized the structure of protein through energy minimization in a spherical water box with 0.15 M NaCl to maintain the charge at neutral using the CHARMM 27 force field, Langevin force field...

07 August 2018 7,008 5 View

How to find out exact percentage of the individual isomer in racemic mixture?

Recently I synthesized the 3-substituted 3-amino oxindole starting from ketimines derived from isatin. After close examination, I come to know that the final product is in the racemic form. I want...

04 May 2018 7,820 3 View

Does the allene and alkyne form of the same compound will show similar or different physical properties?

Recently, I tried to synthesize one organic intermediate having carbon-carbon triple bond. After recording its proton NMR, I came to know that it has a small amount of allene form also. My...

11 December 2017 7,163 3 View

Is it possible to identify the number of isomers in a diastereomeric mixture of an organic compound by Differential Thermogravimetric Analysis (DTG)?

I have one drug candidate in diastereomeric mixture. Is it possible to identify the number of isomers in diastereomeric mixture by using the second derivative calculations and Gaussian curve...

11 December 2017 821 4 View

How to use FTIR and NMR tools to study the solvatochromic effects of dyes in CMC (critical micelle concentration) study?

I am studying the effect of solvatochromic dyes on the micellization of mixed catanionic surfactant mixtures in a various medium. I am new in this field; kindly provide me step by step protocol...

07 August 2017 3,345 4 View

How to check that the molecular sieves (4A Beads) cannot be reused further?

In organic chemistry we use molecular sieves (4A Beads) for drying of organic solvents. I want to know how to confirm the threshold limit beyond which the molecular sieves (4A Beads) cannot be...

04 May 2017 7,089 6 View

Is there any free or open source data analysis software that does quantification of LC/MS data exported in .lcd format?

I have recently analysed the organic molecules, using Shimadzu LCMS 2010A (Japan) by positive electron spray ionization mode. This instrument exports files in .lcd format. I tried mMass and...

04 May 2017 3,172 3 View

Racemization in amino acids?

01 February 2017 174 13 View

TGA and DSC curves of diastereomers in racemate form?

I recorded the TGA and DSC of few active pharmaceutical ingredient (API). Out of 14 samples, the ten samples contains the enantiomeric racemate; while four samples are in diastereomeric racemate....

31 December 2016 7,218 2 View

How to calculate critical micelle concentration by NMR?

07 August 2016 6,641 7 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

How the parameters (such as Mw, Chemical bonds, polymer bland and so on) affect the mechanic property of polymer (such as storage, loss modulus) ?

Anyone can recommend any books on such topics? Thanks in advance.

02 March 2021 8,457 2 View

How do I determine the degree of polymerization of PEG 400 based on NMR integration?

Hello, I am working on the photocatalytic degradation of PEG 400. I would like to know if it's possible to determine the degree on polymerization based on NMR integration, or by the MW of the...

02 March 2021 6,186 3 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View