How to run MD simulation for metallo enzymes having zn in GROMACS?

I want to do MD simulation for metallo enzyme as well as protein-ligand complex in GROMACS. But when i use the pdb structure with zn ions it showing error. Help me to sort out this problem. Which...

10 November 2016 4,488 4 View

If a PDB coordinate file has missing residues. How can i repair the protein?

suggest tools to repair missing residues in PDB coordinate file

05 June 2016 2,694 2 View

How can I rectify the following error in Gromacs?

In grompp in ion.trp filr creation there occur error. Fatal Error, Too much Warning (1), use option -maxwarn. could anybody tell me how to use this option, if i use this option its asking for...

02 March 2015 9,217 3 View

In GROMACS when I give a PDB file its showing the error that HE1 atom not found in topology. How can I rectify it?

gromacs forcefield error

02 March 2015 7,032 2 View

Can anybody send gromacs tutorial for protein - ligand complex MD simulation in ubuntu?

gromacs tutorial for simulation

02 March 2015 3,737 0 View

How can I rectify the following GROMACS error? Fatal error: Atom HB3 in residue SER 3 was not found in rtp entry SER with 8 atoms while sorting atoms.

rectify my error Fatal error:Atom HB3 in residue SER 3 was not found in rtp entry SER with 8 atomswhile sorting atoms.

02 March 2015 1,600 10 View

How can I get a protein-ligand complex from sybyl x 2.0 for MD run and how can we separate the ligand from the protein?

sybyl x protein - ligand complex

02 March 2015 210 2 View

Why are we adding hydrogen, removing side chains and removing ligand substructure in molecular docking?

I'm referring to molecular docking sybyl version 2.0

09 October 2014 8,334 5 View

How to calculate the fraction metabolized of a drug by an enzyme using clearance(ml/min) values of the metabolite formed?

I am trying to find the fraction metabolized of a drug by CYP and UGT enzymes. I am unable to get the values of fraction metabolized (Fm) directly from the literature. Can we calculate the Fm of a...

21 February 2021 5,379 2 View

How long does it take to design and validate transition state analogue inhibitors?

Hi, I'm asking from the point of view of designing a research plan: How long (approximately) can it take to determine the transition state structure of an enzyme substrate using kinetic isotope...

14 February 2021 2,610 1 View

Kinetics of Enzyme production in Recombinant E Coli?

Hello, I am trying to find kinetic information (such as rate of enzyme production etc.) on the expression of taq polymerase in E-Coli after inserting a recombinant plasmid. Any help would be...

12 February 2021 1,386 3 View

Help with Amyloid beta detection protocol (western-blotting)?

Hi everyone, I am a first year PhD student working on amyloidosis. I would like some tips and tricks to crack efficiently my current nightmare, i.e. the western blotting of the Amyloid beta and...

11 February 2021 2,513 3 View

No title

Hello! I want to determine the activity of my in house Reverse Transcriptase enzyme. For this, I have used Thermo's Enzcheck Reverse Transcriptase assay kit. I used commercial Thermo RT enzyme to...

08 February 2021 7,285 1 View

How define one baker unit(BU) is the amount of hydrogen peroxide catalase ?

07 February 2021 2,006 1 View

Does DNA A-tailing survive after agarose gel electrophoresis and purification?

Hi everyone, I need to clone in pGEM-T vector the result of amplifying a metagenomic library by PCR with a high fidelity polymerase but I only want to clone the fragments of an specific size...

04 February 2021 6,051 8 View

What are some common oxidants used to oxidize iron sulfur clusters in proteins for techniques like EPR?

I have used potassium ferricyanide (which is likely the most common) extensively in the past, but I am curious to know if there are other oxidants that work well. I need to generate the oxidized...

29 January 2021 9,803 4 View

Papain Enzyme Assay...?

Hi all, I would like to know how can I estimate the activity of the enzyme, papain, which is used in reactions as crude latex extract of papaya. Please share some procedures if anybody having...

26 January 2021 569 4 View

Where can I find plants pyr-GC-MS data?

25 January 2021 5,403 2 View