11 Questions 13 Answers 0 Followers
Questions related from Ladan Mafakher
hi, I have a PDB file of small molecules as chemical compounds (Figure 1) but I want to know their atom type like the PDB file of similar small molecules which has atom types such as CA, CB, ......
02 December 2023 203 5 View
Hi every one I have a peptide library (around 300 peptides) that I would like to dock peptides to its target while I want a high throughput molecular docking webserver or software to do this. Does...
08 October 2023 7,485 5 View
Hello everyone, I have a peptide library I want to filter my peptide library based on the stability and solubility of peptides. The Protparam webserver does not give a library of peptide files to...
25 September 2023 9,157 0 View
I have Gromacs 2019. when I want to run mdrun by GPU command I faced this error " Fatal error: Unexpected cudaStreamQuery failure: an illegal memory access was encountered. what is the problem and...
20 September 2023 6,021 0 View
Hi everyone I want to model antibody structure but I do not have the sequence of the whole antibody. I just have the sequence of its CDR region. Do you know any web server to model antibody...
17 September 2023 6,776 2 View
hello I want to make 2-dimensional plot like a picture as I attached I do not know how I can make it by gmx rms command in gromacs. could anyone help me with this issue?
24 October 2021 9,362 2 View
hello I want to measure free binding energy by gmx sham. but I do not know what is graph.xvg, gibbs.xvg and esham.xvg as input files in this command, and how I can generate...
24 October 2021 6,115 0 View
hello i want to install mpijava on ubuntu 16.0.4 for osprey i downloaded mpiJava1.2.5x i installed JDK1.6.0_45 in /usr/lib and after install jdk i type follow command to path to bin export...
19 July 2017 9,036 1 View
hello i did docking by cluspro on my receptor and ligand that both of them have been modeled by modeller according to crystal structure of their template. both of my molecule have up to 30%...
18 February 2017 2,740 3 View
hello i have problem in analysis dssp plot. i have 117 amino acid in my protein structure but dssp plots show me 100 and 70 amino acid. i do not know why? pls help me. thanks a lot
27 December 2016 1,513 6 View
can i use b-actin as control gene in real time PCR? because in articles that i have, they use GAPDH as a control for real time pcr and b- actin for western blot. i do not know why and what is...
02 May 2016 5,896 10 View
