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Questions related from Saleha Hafeez
Program: g_mmpbsa, version 2024.1 Source file: extrn_apbs.cxx (line 152) Fatal error: Failed to execute command: $APBS pybYcUWA.in --output-file=pybYcUW.out
08 August 2024 5,942 0 View
I performed mmpbsa of protein-protein complex simulation on gromacs. My binding free energy is +166781. This complex is stable when experimentally produced in wet lab. In index.ndx I grouped...
20 July 2024 4,099 5 View
We produced scFv of an antibody from bacteria. Now we want to establish dissociation Kd of antibody using quantitative elisa. How can i know the expected Kd value (range in nM, or mM)?
05 June 2024 2,479 5 View
If we design proteins like tetrabody or triabody with unique binding sites in silico without further wet lab validation can we patent that structure and procedure?
02 June 2024 2,475 1 View
My simulation suddenly stopped due to some reason. Now i cannot restart the simulation from previous checkpoint because it was not written properly. my _prev.cpt file is also corrupted....
19 April 2024 2,439 0 View
Please suggest bioinformatics journals which do not need wet lab experiments.
11 March 2024 2,785 6 View
We want to simulate a protein-cabohydrate complex at various pH ranging from 6.8 to 7.4. Can we do this on Gromacs?. Do we have to simulate complex at different constant pH or the system will...
06 March 2024 1,582 3 View
Histidine can adopt 3 protonation states: HIE, HID and HIP. Which protonation state will it adopt at ph 7.4
21 February 2024 8,478 0 View
Agglutination of RBCs is normally caused by IgM antibodies. Is there any case in which IgG antibody caused the agglutination of RBCs?
02 February 2024 3,521 2 View
For example We have 10ul RBCs and want to know the total number of Antigen X on 10ul RBCs.
25 September 2023 1,471 2 View
I have a single purified sample of trimer, dimer and monomer proteins purified through affinity chromatography. Is there a way to find concentrations of each protein in a sample? If total...
20 June 2023 2,725 7 View
Can we use any whatmann filter papar or any other thick cellulose filter paper in western blotting?
10 June 2023 2,588 0 View
We are inducing a periplasmic protein using 1mM IPTG at 37 degrees for 3 hours. We cannot centrifuge and remove supernatant the same day. So can we store the broth containing Bacterial cells and...
07 May 2023 7,729 4 View
In DNA gel electrophoresis my plasmid DNA is above DNA ladder which indicates nicked dna. Plasmid was purified by plasmid miniprep kit. My plasmid is not digesting. Enzymes are fine. Agarose...
08 November 2022 1,181 3 View
My protein is scfv 25kda which precipitates after puirification through ni nta chromatography. Protein precipitation is observed next day when protein is taken out from refrigerator. Is there a...
06 October 2022 3,152 4 View
Is there a way to break homodimer scfv and allow it to form a monomer scfv? Is there a way to convert homodimer scfv into monomer scfv consisting of 2 disulfide bonds at interface of dimer?
19 September 2022 3,213 2 View
Discovery studio is showing metal acceptor bond between ligand protein. What is the nature of metal acceptor bond? Bond is between iron of ligand and oxygen of protein Fe3O4 is the ligand
16 July 2022 3,267 0 View
Dear All, I docked a ligand using Autodock vina and performed MD simulations for about 100ns. I need help in analysis of the results. If we see the results can we say the ligand detached from...
01 April 2022 1,483 3 View
I have to simulate carbohydrate-protein complex on GROMACS. I have used GLYCAM webserver to generate a trisaccharide. Then I used acpype of Ambertools21 to prepare carbohydrate ligand using...
01 March 2022 5,950 6 View
I am new to MD simulations. Large movements in proteins occur at microsecond or more timesteps. My question is which one is timestep dt or nsteps?
24 December 2021 6,576 4 View
Can we use AmberS99 for antibody (protein) and Charmm36 for antigen (drug like small non-protein) in md simulations? Or do we have to use only one forcefield for both?
08 December 2021 2,046 3 View
I am using Ubuntu 20.04 LTS on Windows 10. Problem is Ubuntu is not detecting any of my GPUs. I was working on Gromacs and when I tried to run simulations on GPU it said GPU not detected. Gromacs...
28 October 2021 7,319 4 View
We used playmolecule to protonate the protein at pH 7.4. Gromacs adds hydrogen atoms. Is there a way in which we can prevent this addition and use the molecule as it is?
27 October 2021 6,768 4 View
We have to compare two proteins (wild type and mutant) Do we have to first perform protein stability test in water MD simulation and after that for function, protein-ligand simulations? Will...
22 October 2021 941 4 View
I am getting this error. Nonbonded interactions on the GPU were requested with -nb gpu, but the GROMACS binary has been built without GPU support. Either run without selecting GPU options, or...
22 October 2021 918 0 View
We are going from protein sequence to protein structure. Does MD simulation refine the protein structure? if we have to perform MD simulation then do we have to perform loop modelling and protein...
21 October 2021 1,311 4 View
We have to use E. coli only to produce Trispecific scfv of size 100kda Problem is that E. coli is not good with the expression of large proteins. Is it possible that we use N terminal signal...
31 July 2021 2,387 1 View
ORF1a is a non structural protein of SARS-COV-2. It has 4550 amino acids. Is there a way to predict the whole protein complex?
10 May 2020 6,923 0 View
I want to stain liposome with rhodamine. For this I need protocol.
21 April 2019 7,284 1 View
I am getting same UV-VIS spectrum of Magnetite nanoperticles no matters how much I sonicate.
03 March 2019 4,167 2 View
I am using probe ultrasonicator to disperse MNPs in ethanol for SEM.
26 January 2019 2,204 8 View
I have to make 200-350nm magnetite nanoparticles by solvothermal method. Magnetite particles of this size show ferrimagnetic properties.
20 January 2019 2,763 4 View
