24 July 2013 1 6K Report

I have always used VectorNTI, I am happy with it, I am asking because I have not used anything else and am curious if anyone has ever compared it other programs.

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Autodock Raccoon - the following maps are missing?

I've generated a set of maps for my receptor using ADT (AutoDockTools). It has resulted in the files: .A.map .C.map .HD.map .N.map .NA.map .OA.map .SA.map .d.map .e.map But when I try loading the...

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How to specify binding sites in AutoDock Raccoon?

Hi all, There are two big questions here. I am extremely grateful for even the smallest contribution that yields a result. This is concerning Raccoon(1) original, not Raccoon2. The original...

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How to run AutoDockTool's Autogrid4 command?

Hi all, Please imagine this to be a brand new machine with the latest installation of: Autodock Vina Autodock AutodockTools (MGLTools). I'm following a Nature Protocol for the prediction of...

14 December 2020 2,191 3 View

How do I retrieve every CID from pubchem?

Hi all, I guess there are probably several ways of doing this. I'm looking to get access to every Pubchem CID. All compounds are published for download, but the files are quite large in size and...

01 November 2020 8,612 3 View

Platelet Counting on Flow Cytometry?

Hi, Does anyone have a method for counting platelets on flow cytometry (cytometer=Cytoflex) without the need of using TRUcount beads or reference beads? Is it possible or do I need to purchase...

23 September 2020 3,509 1 View

How to get hydrogen bond analysis using MDAnalysis working with custom atom names?

Hi, I'm up against a horrible deadline so I'm hoping for some help figuring out what I'm doing wrong. I have a list of custom atom names in Gromacs of which I want to perform hydrogen bond...

10 January 2020 7,505 6 View

How to resolve GROMACS mdrun seg fault during minimisation?

I'm waiting on email conformation for the GMX user group, but this is in reply to Reviewers so I'm pressed for time and asking here. I'm building a small collagen-based system. The crystal...

13 November 2019 5,517 10 View

Are these QC DFT settings appropriate?

I'm picking up quantum chemistry after a three year break. I've forgot a lot and I'm now using ORCA (version 4.0.1.2). My system is a non-enzymatic chemical reaction between lysine, arginine...

30 August 2019 3,966 2 View

How to calculate whether a disease outcome in a population is by chance or significant?

Hello all, I have a huge dataset of longitudinal medical records. Each record contains indications for drug and disease. I have been able to calculate the Cure Rate in the population given a...

04 October 2018 2,529 3 View

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