Why is PyRx changing my ligand element after molecular docking ?

Alfred Wei Lin Chuah @Alfred-Wei-Lin-Chuah

20 March 2024 0 5K Report

I was using PyRx Vina Wizard to perform ligand-protein interaction molecular docking. However, after loading the results into DSV, I noticed that the elements had changed following the molecular docking process. Has anyone else encountered this issue and found a solution?

I have attached the result file below.

Badges
Science method

More Alfred Wei Lin Chuah's questions See All

Do we need to write protocol for a second study of a systematic review that has been registered and published?

I have conducted and published a systematic review and meta-analysis research with the topic related to public health and health pomotion (protocol was registed in PROSPERO). Now we want to...

03 March 2021 8,920 3 View

Interested to stain mice tissue with WGA 488 conjugate, anybody has a protocol to recommend?

Interested to stain mice brain tissue with WGA 488 conjugate, appreciate if anyone willing to offer me some guidance or suggestions! Thank you!

28 February 2021 3,951 2 View

Where can the fault diagnosis data set of lithium battery be found?

Most of the data sets on the network only contain good information about the voltage and internal resistance of lithium batteries. The data of faulty battery is missing. Who can help me, I will be...

21 February 2021 8,659 1 View

How do I collect online measures in a same-different task?

The same-different task requires to subjects to indicate whether a pair of stimuli seen or heard are the same (say AA or BB) or different (say AB or BA). Researchers often collect offline measures...

20 February 2021 9,226 2 View

How could I get the P-value from the mean, SEM, and n of different groups in the t-test?

How could I get the P-value from the mean, SEM, and n of different groups in the t-test without the original data? For detail, I would like to know the P-value between BMP-2: 50ng/ml group and the...

06 February 2021 6,539 4 View

Why are my western blot bands so distorted?

Hi guys I'm out of ideas here please help! I've never had consistent problem like this doing westerns before and I can't figure it out. The condition used: - First 4 lanes have 50ug protein in...

04 February 2021 2,297 3 View

When is it optimal to choose an OFAT (One factor at a time) design over DOE (design of experiment)?

As a current undergraduate student majoring in Microbiology who is still learning DOE (Design of experiment) on my own, I have heard and read that an OFAT design is considered the most inefficient...

29 January 2021 8,256 3 View

Can Dess-Martin Periodinane be used in DMF or THF?

After seeking for references, most of the solvents for Dess-Martin is DCM, but my compound has a poor solubility in DCM. Because my compound is acid-sensitive, I prefer not to use IBX to oxidize...

17 January 2021 3,586 3 View

What are the possible drawbacks of using miRNA sponge to enhance the specificity of gene expression?

I am searching for miRNA repeats put between WPRE and 3'LTR of my lentivirus, in order to enhance the specificity of transgene expression in human neuron cells. But if clinically translation of...

26 December 2020 9,921 2 View

Can Apparent Activation Energy determine Conversion Rate in a catalysis reaction?

Recently, I got a concept that is contrary to my understanding from two papers. It can be described as follows, in brief: There are two catalysts for the same reaction, on the catalyst with higher...

09 December 2020 2,406 28 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

Does anyone know HRM channel in a 2 plex QIAGEN Rotor- Gene Q qPCR can be used as a separate channel?

I am going to have 3 different probes in my qPCR work that I am going to do. But I realized that the machine we have in the lab is a Rotor-Gene Q 2plex HRM Platform, saying it has green, yellow,...

01 March 2021 8,544 1 View

In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein?

Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...

01 March 2021 8,747 4 View