31 March 2023 0 5K Report

Hello all,

I have 1000 frames and i want to calculate the binding pocket volume of the protein using CAVER 3. Can someone help regarding the creation of configuration file for the same to execute the program? Is there any way possible to mention the residue number in configuration file and the program will calculate volume around those residues ?

I read the documentation and i found out most of the configurations they have provided is for calculating tunnel, are tunnel and cavity same?

Any help or suggestions would be greatly appreciated.

More Smit Patel's questions See All
Can anyone suggest me broad host range fluorescence expression vectors for Gram-positive bacteria ?

Hi everyone, I am looking for fluorescence expression vectors for expression in gram-positive bacteria present in the skin microbiome. I need to tag them with a fluorescence marker and observe...

06 February 2021 2,566 4 View

No title

11 January 2021 3,284 3 View

How can we count the number of edges in an edge detected image using canny/sobel algorithm in MATLAB?

I need to process an image for edge detection and then want to count the number of edges in that image.

29 December 2020 5,594 2 View

Which are the vendors who sell commercial SWIR (NIR-II) dyes?

I am searching to find commercial vendors who sell SWIR dyes. I could only find Nirmidas Biotech which sells different NIR-II dyes!

23 December 2020 5,002 3 View

How to get doi of presentation ?

doi of your presentation in the conference

23 December 2020 9,370 2 View

Precipitation of Pcl from polymeric solution ?

We working on PCL nano particles 1).Ketoprofen (10mg)+ dmso(5ml) Pcl (10mg)+ DCM(5ml) 2).Water 10 ml+ 10 mg When we mix both 1+2 after solublization (400 rpm) Why precipitation of polymer occurs?

09 December 2020 5,033 11 View

How to induce doxorubicin resistance in MCF-7 and MDA-MB-231?

I want to establish DOX/R cell line in vitro for the research study.If any one suggest the protocol then it would be a great help.

03 December 2020 9,795 5 View

What are the conditions under which we should choose logit model instead of mixed logit model?

I developed logit models for mode choice behavior using a questionnaire-based dataset. However, a reviewer suggested me to go for mixed logit models. I do understand that mixed logit model solves...

22 November 2020 967 6 View

What is the difference between weak from Ritz method and variational form Ritz method while solving a boundary value problem ?

What is the difference between weak from Ritz method and variational form Ritz method while solving a boundary value problem ? Can all differential equations take variational form ?

18 November 2020 2,341 2 View

What could be the reason for a broad peak of ADC(Antibody Drug Conjugates) using HIC-UV method (Hydrophobic Interaction Chromatography)?

Hi, We are working on DAR (Drug to Antibody Ratio) estimation of ADC using the following HIC-UV method. For some of the unconjugated mab we getting a sharp peak but for our desired mab we are...

15 November 2020 7,359 0 View

Similar questions and discussions
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

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

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

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

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 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 get onecolumn document from standard IEEE ACCESS LateX template?

I have prepared a manuscript in IEEE Latex template, but for some purpose, I need to prepare a word file as well (detailed format is not required). Compared to two column .tex file, one column...

02 March 2021 1,830 3 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

Our partners will collect data and use cookies for ad personalization and measurement. Learn how we and our ad partner Google, collect and use data. Agree & close