55 Questions 79 Answers 0 Followers
Questions related from Ibrahim M. Ibrahim
i am trying to use ADFR to perform docking, however, i found some parameters in the running command that can affect the searching. two of these commands that i dont understand the difference...
12 November 2024 9,440 0 View
i have a tetramer protein with one calcium ion bound to each monomer. I have started the production run without any restraint at first, however, the ions left their binding site. So i added a...
23 September 2024 3,389 1 View
Are there free databases of peptides?
24 November 2022 3,594 3 View
I have a single receptor and I have docked many compounds to it and I want to perform funnel metadynamics to the best three compounds. my question is how to determine the different parameters of...
05 November 2022 1,931 0 View
I have a protein-ligand (glycan) complex and want to do an MM-PBSA analysis using AMBERTOOLS after doing MDS (NAMD). What are the files necessary I should prepare for glycan? Note: I used...
31 December 2020 2,882 2 View
i have run a simulation for a protein (minimization, equilibration and production). in minimization step, the potential energy value in the log file is minimized at temperature = 0 K. in the...
24 December 2020 9,098 3 View
Greetings, I have a peptide with THIOPHOSPHO-SERINE residue from a PDB file. when I tried to use it with CHARMM-GUI webserver to produce the files for MDS, it asked me to upload the CHARMM...
19 December 2020 1,664 3 View
Greetings, I am trying to run GROMACS 2020.3 on a supercomputer using this command to do the production run: mpirun -np 24 gmx_mpi mdrun -v -s AB_md_0_1.tpr -deffnm AB_md_0_1 >...
18 December 2020 1,437 3 View
Is there a webserver or a program that can predict whether a drug is an agonist or antagonist?
01 January 1970 5,190 1 View
Greetings, Nowadays, there are a lot of bioinformatics tools doing the same thing for example Multiple Sequence Alignment, or docking. How should I compare them to select the best one? Also,...
01 January 1970 7,908 2 View
i am using NAMD to do an MDS run on a supercomputer. but i want to know what is the number of cores to use to make it run very faster? supercomputer nodes: 6158 supercomputer cpu-per-node: 32 i...
01 January 1970 3,997 2 View
what are the required numbers for cpu-per-task and ntasks in the .sh file for running NAMD on a supercomputer?
01 January 1970 7,705 6 View
Greetings, i have done an MDS of 100 ns (1000 frames) using NAMD and want to use the MMPBSA script in ambertools20. However, i dont know which interval should i write in the &general part of...
01 January 1970 6,685 3 View
Greetings, I have a question about selecting drugs for docking. I have a protein and I want to dock drugs to it from ZINC15 library. However, my computational resources are limited. So, Is there...
01 January 1970 6,952 2 View
I used AutoDock Vina to dock a drug with a protein. this gave me a list of conformations with the different binding affinities. I selected the more negative one to analyze it using PLIP webserver...
01 January 1970 8,757 3 View
Are there programs that can be used to simulate the motion of water molecules in the brain under some conditions like magnetic field, ...?
01 January 1970 3,547 3 View
Hello! I am still learning MD and found that there are different softwares that can do this job such as GROMACS, NAMD, AMBER, CHARMM, Desmond, and OpenMM. So what is the difference between them?....
01 January 1970 3,213 8 View
I have results from the MDS and I want to cluster them. what are the best methods, and clustering parameters to use? and is there a webserver of open-source programs that can do this? Thank you...
01 January 1970 3,617 6 View
i am trying to solvate and neutralize a system containing more than 99,999 atoms (in my system an atom forms one residue) using VMD. however when i try to use psfgen to generate a segment for it,...
01 January 1970 5,434 4 View
How to run NAMD 2.14 on cores from multiple nodes in slurm? need batch file please. this is the one i am using: #!/bin/sh #SBATCH --job-name=grp_prod #SBATCH --partition=cpu #SBATCH...
01 January 1970 8,137 7 View
I am using CHARMM-GUI to generate the files for MDS for protein-ligand complex and I noticed that the partial charges generated from the webserver for the ligand in .rtf file are different from...
01 January 1970 2,559 3 View
I have a protein with CSO amino acid in its sequence. when i upload it to CHARMM-GUI to generate the MDS files, it asks me to upload CHARMM top & par for CSO or rename CSO to other names. How...
01 January 1970 4,512 1 View
1. Given r(t) and ν(t) at one time point t, first compute the forces f(t) on each atom using the force field. 2. Do an update of the positions: r
01 January 1970 2,646 1 View
Greetings, I have a computational biophysics background and I want to enter the field of Deep Learning. How can I do this? should I read books, research papers, etc..? I know how to program in...
01 January 1970 5,349 4 View
I have performed a lipid membrane simulation only in NAMD using PBC, then used this command to wrap the trajectory (pbc wrap -center bb -centersel membplugin_lipid -compound res -all) the command...
01 January 1970 2,816 4 View
I have done an MDS using NAMD for protein ligand complex and I want to calculate the magnitude of the vector produced from the subtraction of center of mass point of ligand and protein. My...
01 January 1970 4,036 17 View
I have learned the basics of python and I want to learn how to use python with scientific programming. Any recommendations?
01 January 1970 6,447 5 View
I started minimizing a solvated protein-ligand structure with emtol = 1000 then I tried to reduce the tolerance until I reached 100 and it achieved a maximum force of 99.9 with a potential energy...
01 January 1970 9,020 6 View
Greetings, I want to download a library for docking from ZINC15 database but I found that there is a reactivity filter and it contains these names: Anodyne - Bother - Clean - Standard - Reactive...
01 January 1970 4,903 1 View
openbabel can be used to add partial charges to molecules using this command: obabel -i pdb lig.pdb -o mol2 -O lig.mol2 -partialcharges where can be replaced by any type written in this website...
01 January 1970 5,636 8 View
for each P atom in a lipid leaflet, I want to select other P atoms within 10 Angstrom. how can I do this using MDAnalysis? I have tried this: local_p_atoms = u.select_atoms('(around 10 name P)...
01 January 1970 3,316 0 View
I have built a membrane system using charmm gui. How can I know that the system is equilibrated after doing the equilibration steps? What are the values I should monitor to know? Thanks
01 January 1970 8,513 8 View
I have read in some papers that the citrate-capped gold nanoparticles are hydrophilic while in some papers they said that they are hydrophobic. Which one is correct? hydrophilic:...
01 January 1970 6,884 4 View
I have two groups of values one has 13 elements and the other has 32 elements. these values are positive, continuous and not dependent. I want to know what is the best test to use to know if the...
01 January 1970 1,013 10 View
how can I simulate a system containing a nanoparticle and a peptide binding to it in NAMD using a force field compatible with CHARMM36?
01 January 1970 970 7 View
i have performed MD simulation in GROMACS of the apo protein and another one with the same protein but with a ligand and performed PCA analysis as follows: 1- calculate the covariance matrix of...
01 January 1970 8,455 3 View
i have an enzyme that performs an oxidation reaction on a molecule. is there a way to measure the rate constant of this reaction using a type of molecular dynamic simulation? thanks
01 January 1970 5,173 4 View
Is there a tutorial or a paper that decsribes how to perform principal component analysis using GROMACS and how to interpret the data obtained?
01 January 1970 4,467 1 View
i am a beginner in funnel metadynamics and I was following the paper published in nature protocols about FMAP titled: Ligand binding free-energy calculations with funnel metadynamics. i started...
01 January 1970 8,998 0 View
I have made an MDS using NAMD for a protein-ligand complex with periodic boundary conditions (PBC) and I want to analyze the data. what are the steps that I should follow to prepare my system for...
01 January 1970 8,422 4 View
what are the best libraries (in python) or programs to perform network analysis of MD simulation trajectory for discovering allosteric effects? thanks
01 January 1970 7,638 2 View
i used CHARMM-GUI membrane builder module to prepare the necessary files for simulating a membrane using NAMD and while inspecting the configuration input files, i noticed that it uses collective...
01 January 1970 9,339 1 View
I have read a paper (link at the bottom) that uses MM-PBSA calculation for calculating the binding energy for their protein-ligand complexes. However, they only used the last 1ns of their...
01 January 1970 3,450 6 View
I want to perform VS using Autodock vina using a library such as zinc15. Could you please provide me with videos that describe this process from the preparation of protein and ligands to the...
01 January 1970 7,008 11 View
i have a protein that is known to undergo a post-translational modification on one lysine that is responsible for its function (inhibiting the acetylation was proved experimentally to inhibit the...
01 January 1970 4,317 1 View
i have performed MD simulation of a protein and I want to use TICA for dimensionality reduction, since it is better than PCA, using the dihedral angles of the protein. However, one parameter in...
01 January 1970 3,870 1 View
I have a protein that has a loop of missing 7 amino acids and i want to model them. what are the tools (webservers or programs) that can help me in this task?
01 January 1970 1,497 6 View
I have a glycosylated protein and i want to dock it to another protein through the glycans not the amino acids. I have tried HADDOCK but the glycans were broken from each other and from the...
01 January 1970 2,317 1 View
It there a way to build a nanoparticle with citrate on its surface as a capping agent for molecular dynamic simulation?
01 January 1970 3,784 3 View
Hi! I have windows 7 and an installed visual studio 2019. how can I use cmd, cmake(GUI) or cygwin64 terminal to install GROMACS 2019.4 edit: I tried to see this...
01 January 1970 2,459 4 View
Greetings, What is ZINC diversity dataset? and Is there a difference between it and ZINC 15 database? Thanks
01 January 1970 4,610 0 View
I want to implement a python code to perform protein protein docking using fast fourier transform in python with visualization of correlation maps for the two grids for educational purposes. i...
01 January 1970 9,810 5 View
I was following the FFTK tutorial using ORCA as a QM software to obtimize ethanol. the default route in FFTK during geometry optimization is MP2 6-31G* TightSCF opt. However, i read in this review...
01 January 1970 5,975 2 View
i have some compounds with high charge penalty obtained from CGenFF and i was trying to obtimize them using FFParam, however, the atoms that have a high penalty are carbon atoms such as this...
01 January 1970 6,474 0 View
I built a model using swiss model web server from a template and the Ramachandran plot contained some outliers in the active site. My question is, which process should I use to solve this,...
01 January 1970 9,127 2 View
