Homa Ahmadi

15 Questions 35 Answers 0 Followers

Questions related from Homa Ahmadi

How cell wall peroperties of l.lactis may change after surface display of a heterogenous antigen?

Hi there! We are applying L.lactis for expression of a heterogeneous antigen using a cell wall anchor subunit. Cloning process has been verified and expression optimization is up now but I'm...

08 August 2019 6,116 2 View

How can I determine the intact bacterial cell in flow cytometry?

Hi guys! I'm working on a whole cell SELEX project of bacteria for developing a diagnostic tool. Most of bacteria are less than 2 micrometer in size that is interfered with many noises . Please...

03 March 2018 8,202 5 View

Why FITC-nucleotide conjugate emission vanish during SELELX process?

Hi there! I'm using FITC-primer conjugate for amplification of DNA library. The florescent tag is necessary for investigation of SELEX proceeding by flow cytometry technique. The problem is...

02 February 2018 1,756 9 View

How can I optimize a sandiwich aptamer-antibody system?

Hi there!! I have design an aptamer-antibody sandwich ELASA system for a whole cell detection test. Can I follow experiment design process like taguchi designs or should I consider Chequerboard...

09 September 2017 8,704 2 View

Am I allowed to run HCD test with Real-time PCR primers?

Hi guys HCD test is a common test for quality control of recombinant protein in order to investigation of residual Host Cell DNA as a contamination in drugs. Considering 16srRNA repeats in E.coli...

01 January 2017 3,440 0 View

How can I run PAGE for alkaline peptides?

Hi guys I'm runnig poly acrylamid gel electrophoresis for verification of moleular weight of my peptide but it doesnt pepnetrat in gel by runnig SDS-tris-PAGE. Could u plz direct me to a protocol...

01 January 2017 4,353 2 View

How can i install DSSP for gromacs on centos6?

Hi everybody I tried to execute dssp for gromacs 4.5.7 by following this instruction: #sudo wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 -O /usr/local/bin/dssp #sudo chmod...

04 April 2015 4,705 1 View

How long is an appropriate time for structural change investigation by MD?

Hey there! I'm using gromacs software for ligand binding simulation. I want to investigate structural change of protein after complex formation. How long the MD should last to reach the most...

03 March 2015 1,756 8 View

Why the h-bond may vanished during ligand binding simulation?

Hi there! I have performed MD simulation for protein-ligand binding. I used g_hbond command for protein and ligand interaction analysis. I observed that h-bond numbers reached from 4 to 0 after...

02 February 2015 8,256 8 View

Why is there a disparity between c-alpha elements and amino acid content?

Hi every body I was going to calculate RMSF for residues of protein after simulation. I chose c-alpha group which contained 667 elements. My protein has 679 amino acids and 50 of them are Gly. So...

02 February 2015 1,354 9 View

Any advice on binding energy calculation by Gromacs MD?

Hi everybody; I have performed MD for protein and protein-ligand distinctively by Gromacs 4.5.7 but I didn't state the free energy computation parameters in .mdp file. Is there another way to...

02 February 2015 1,199 5 View

How can I set number of steps for nvt equilibration?

Hi Is there any approximation for setting steps in nvt and npt equilibration? I'm gonna do simulation for a protein in water.

01 January 2015 2,288 6 View

Can anyone help me to resolve the following automated topology builder error for submitted pdb file?

Hi everybody! I'm using ATB to create .itp file for gromacs MD and I have repeatedly received this error message: "the submitted molecule has a critical connectivity missing or contains more than...

01 January 2015 257 13 View

Free space on a device for gromacs MD?

Hi I'm working with a restricted free space on a system. How can I aproximate the volume of result for MD? Can I reduce the output on .mdp file if it's needed?

01 January 2015 2,576 4 View

Gromacs installation on centOS cluster error, help please?

I'm trying to install gromacs on linux cluster centos6. After successful installation I got an error for not finding pdb2gmx command. It seems like that it is for not addressing executable file...

12 December 2014 2,163 1 View