10 Questions 6 Answers 0 Followers
Questions related from Zahra Sadat Eslami
Hi everyone I try to perform equilibration on my system in AMBER16. I use pmemd.cuda and follow AMBER tutorials. This step is interrupted during execution and remains incomplete. also I have the...
09 July 2021 5,738 0 View
Hello I want to make input files for Amber package to run molecular dynamics simulation. I don`t know how can i find references for choosing Histidine protonation state and N- and C- terminal...
30 May 2021 9,376 2 View
Hello I try to install and run the VMD software on windows 10 (64-bit).It doesn`t work and it is closed when I run it. I checked all of tutorials, videos and documents. But they did not work...
23 February 2021 8,502 3 View
Hello I try to amplify gene of interest by RACE-PCR. For 5` RACE, I saw multiple bands after using specific nested primer. But The desired band was not seen on the gel. What is the reason? When I...
01 November 2020 7,853 6 View
Hello I work with Roche RACE PCR kit and I have a problem with 5` RACE PCR. When I checked my PCR product on Agarose gel, I only saw an unspecific band. I`m not sure about dA-tailing step,...
14 September 2020 9,432 0 View
Hello I want to do MD simulation on a protein model to refine its structure. My protein structure have both folded and intrinsically disordered regions. What force field should i choose for this...
24 August 2020 9,511 5 View
Hello I try to do molecular dynamic simulation with GROMACS software and I work on an enzyme in a plant producing a medicinal secondary metabolite. When i was searching to find a appropriate force...
01 August 2020 303 5 View
Hello I used high fidelity enzyme in my PCR and I saw smear on agarose gel. I repeated the PCR with different amounts of cDNA. But I did`nt get a sharp band. what should i do to resolve my problem?
30 July 2020 3,609 10 View
I try to make a model with MODELLER software and I decide to use multiple template modeling method. Two template structure I choose for my work, have similar Identity percentage (42.54% and...
04 May 2020 1,377 3 View
Do you know any method to distinguish small target band of primer dimer? ( They have similar size.) I tried higher concentration of agarose gel and longer electrophoresis run time. but i didn`t...
23 December 2019 507 9 View
