21 Questions 18 Answers 0 Followers
Questions related from Ayesha Fatima
Dear all, I have done md simulation of ssDNA on gromacs. Now I would like to determine the base stacking parameters such as rolling, twisting, tilting of two adjacent bases. However, all the...
30 January 2024 9,774 0 View
Dear All, İ want to prepare a library of compounds for virtual screening. But I keep running into multiple issues that are already resolved but when I apply the solutions on my compounds, nothing...
25 October 2023 1,987 1 View
Dear All, I am trying to simulate a dimer and would like to restrain a part of it on both chains. not a problem and the error is commonşy reported. so i tried all teh suggestions but none is...
16 October 2023 2,071 2 View
Dear All Many thanks for taking interest in my questions. I am trying to do a PCA analysis of my md simulated structures that are homodimers. I am using gromacs 'covar' command to do it. I am...
04 October 2023 4,482 0 View
Dear all, I have been trying to create a complex for MD simulation in gromacs of Calcium sensing receptor venus fly trap domain with tryptophan in the binding site as it is part of the crystal...
11 September 2023 9,154 1 View
Dear all, I just downloaded the tranches from zinc 20 database. but the files are in gz format. this means each on of them has to be extracted. is that correct if yes then extracting data from...
19 August 2023 9,245 2 View
Hello everyone, I am trying to convert the LOTUS database into pdbqt molecules from sdf as well as smiles. I have tried openbabel as it is the goto software. but it gets stuck if it encounters...
18 August 2023 248 3 View
Dear all, I installed the latest Vina version on my conputer and as everyone knows, it does not have the log file generation argument. so we have to do it manually. Previously, Dr. Muniba of...
25 July 2023 4,490 3 View
Hello all, İ am trying to install mgltools on my ubuntu desktop but i keep getting this error ............................ installing mgltools to /home/bilsab/cadd installers/mgltools x86_64 linux...
15 December 2022 8,988 2 View
Dear All, I am trying to simulate Fe hydrogenases. however, I am unable to parametrise the FeS clusters. There are 4 different types : Fe3S4, Fe4S3, Fe4S4 and Fe attached to Carbon and Nitrogen....
08 February 2022 8,649 3 View
Dear all, I am trying to run an enzyme system nad have to determine the rate of oxygen diffusion into the system. I have the enzyme without oxygen and have read papers where they say, it was...
27 September 2021 8,088 0 View
Good day to all. I am running the g_mmpbsa module from Rishi Kumar I am getting this issue. I think it may be related to python. I have python 3 installed in my system python -m ../MmPbSaStat.py...
22 July 2021 8,162 3 View
Dear all,I am trying to do the mmpbsa analysis on a 1ns trajectory. when i run MMPBSA.py i get the following error..............................................Loading and checking parameter files...
22 January 2021 3,319 1 View
Dear All, I would like to ask if anyone knows of any server that can give the gromacs 53A6 ff topology. I have to prepare my protein in that topology and use it. The ATB server is now only fixed...
13 June 2020 8,209 0 View
Hi all, Does anyone know how to install the g_mmpbsa. I followed the steps by downloading the programme from github, and installing it as given on the software page. However it stalls at sh...
29 November 2019 9,603 2 View
Hi all, i want to dock protein into a receptor that has cofactor in it. I want to determine the effect of cofactor on binding. i looked around the web servers but all remove the cofactor. I found...
10 October 2019 8,180 3 View
Dear all, some time ago, I posted a query on the qm/mm methods but since i managed to solve it, i did not return to the forum. my apologies and thank you to people who followed the question. I am...
24 November 2014 4,887 0 View
I am trying to run a QM/MM in Amber on a protein-ligand system. I have looked for tutorials but they don't explain a few things such as how to heat your system and equilibrate it before MD. Then...
25 October 2014 9,215 3 View
Hi. I am trying to check whether multiple copies of the same ligand can bind in a stable conformation to a protein. I know many people have done this but I can't find the exact protocol. I have...
16 September 2014 249 4 View
I am working on inhibitors of human Wnt proteins in breast tumor. Does anyone know of a resolved structure of a Wnt protein available for download. Pdb does not have it. I checked prosite but...
31 May 2012 9,806 5 View
Dear all, I would like to know if anyone has experience with doing MD simulation of nucleic acids or proteins in high density liquids. I would appreciate if I could be guided to some reading...
01 January 1970 7,015 2 View
