GROMACS Protein Error?

I'm getting following error while pdb2gmx: Residue 2 named LYS of a molecule in the input file was mapped to an entry in the topology database, but the atom CG used in that entry is not found in...

09 October 2019 6,929 2 View

Amber MD error?

I'm getting following error in Amber: > loadoff drug.lib Could not open file drug.lib: not found Could not open database: drug.lib Please help!!

06 July 2019 8,642 2 View

AMBER Antechamber Error?

I'm getting following error while executing following command: antechamber -i drug.pdb -fi pdb -o drug_bcc.prep -fo prepi -c bcc -s 2 Error: cannot run "/home/anwesh/softwares/amber14/bin/sqm -O...

06 July 2019 2,727 2 View

Analysis and Phylogenetic tree for a fasta file?

I have a *.fasta file through nanopore sequencing (Min Ion) of approx ~250MB. I'm having problem in its analysis via MEGA Software due to large file size. I need to select a particular bacterial...

05 June 2019 5,003 6 View

Molecular Dynamics Simulation of MetalContaining Ligands?

I'm currently working on metallic ligands (transition metals/complexes as ligands). For their MD Simulation, how to generate topology for ligand, kindly help?

04 May 2019 5,705 1 View

How to set up QM/MM calculations in Gaussian for Drug-DNA complex?

I have completed molecular dynamics simulation of some drug-DNA complexes, now I need to perform QM/MM calculations on the system. Please tell me as to how to set up a QM/MM calculation in...

09 October 2018 2,226 3 View

Regarding Data Mining Softwares?

Is there any software which could mine data from downloaded research articles (pdf format) as per one's requirement?

09 October 2018 3,897 5 View

Regarding MMPBSA Calculations?

Is there any methodology to increase the no of cores (for faster computations) being used in the command line for mmpbsa claculations: g_mmpbsa -f md_0_1.xtc -s md_0_1.tpr -n index.ndx -i...

06 July 2018 248 5 View

Regarding MD via AMBER?

I am performing MD simulation for drug-DNA complex using GROMACS via AMBER force field. At following step, the program shows an error: gmx genion -s ions.tpr -o solvated.pdb -p topol.top -pname NA...

04 May 2018 5,384 2 View

Regarding MD Simulation analysis?

Can someone let me know about what is and how to perform, Umbrella Sampling in Molecular Dynamics Simulations, performed via GROMACS?

04 May 2018 6,799 5 View

Polymer composites suddenly solidifies?

I am making polymer composite by solvent mixing method. When I am trying to add filler solution in polymer solution it quickly get solidified. How to make them then uinform? It doesn't give time...

03 March 2021 7,540 4 View

What solvent can I used for Paal Knorr reaction between 6-amino hexanoic acid and 2.5 hexanedione?

I am try to make the Paal Knorr reaction between 2.5 hexnedione and 6-amino hexanoic acid, my problem is type of solvent to use, because 6-hexaminohexanoic acid is soluble in water but I am not...

02 March 2021 4,443 2 View

How to polymerize TEOS?

I want to polymerize TEOS on a surface. I know that NH4OH is a preferred catalyst and an alcoholic solvent should be used .But I can not find certain amounts of each material to use. Does any one...

02 March 2021 1,404 6 View

How can extract ciprofloxacin hydrochloride disolve in water er to organic solvent such as dichloromethan or any other solvent?

I need a procedure to extract the ciprofloxacin hydrochloride from aqueous solution by using dichloromethane in detail,. I thank you very much.

01 March 2021 4,306 1 View

How to separate water from glycerol solvent in a solvent recovery vacuum distillation column?

I am currently doing my third year design project. I have been assigned to design a glycerol recovery column in vinyl acetate monomer production. The process unit before the recovery column is an...

01 March 2021 9,525 4 View

How to make fractions of chloroform extract of plant, using seperating funnel?

28 February 2021 8,466 2 View

Why am i not getting solid after reacting APTES with salicylaldehyde?

The reaction of APTES with salicylaldehyde in ethanol leads to the formation of imine compound yellow solid which is mention in literature, but I am not getting yellow solid I don't know why? when...

28 February 2021 2,955 2 View

can I treat waste water containing solvents and alcohol with electrocoagulation?

there are solvents and alcohol in the waste water of a factory that produces disinfectants. Increasing this waste water requires very serious operations. Can I treat this waste water with...

27 February 2021 2,609 3 View

How to replicate the well conditions of a crystal hit with 20%(w/v) isopropanol?

I had a crystal hit in a well with 0.1M HEPEs pH 7.5, 10%(w/v) PEG 4000, and 20%(w/v) isopropanol. Why is isopropanol in w/v here if it's just solvent? How do I recreate this well condition?

25 February 2021 9,761 1 View

How to increase solubility of Poly acrylic acid in Dioxane solvent?

I am working with Polyacrylic acid (100.000Da) and instead of water, I need to use another solvent (dioxane) to dissolve PAA. However, because of the high molecular weight, it's quite hard to...

25 February 2021 2,225 5 View