Percentage of potential SASA of ligands in Gromacs??

Dear All, How to determine the SASA of different ligands in absolute values and percentage of their potential SASA in solution to estimate how buried they are in GROMACS. Thank you in advance.

03 April 2019 6,200 2 View

How to generate the wfn file in gaussian ?

Hi all, I have gauss view (6.0.16) and gaussian16W for microsoft windows. I want to generate the wfn file. I have tried specifying of C:\path\molecule.wfn in molecular specification section...

11 December 2018 7,311 0 View

How to guess time taken to complete a QM/MM job in gaussian ?

Hello everyone, I have run optimization of protein-ligand complex using QM/MM in gaussian. I did not find any criteria to find how much time will be taken to complete this job. Is there any...

10 November 2018 9,208 0 View

Suggestion for combing of processors on server??

Hi everyone, We have HP server consist of 160 processors on 80 cores (i.e. each core has 2 processors). We want to utilize this server for molecular dynamics work. So we want to combine like 60...

02 March 2018 2,608 0 View

Error in generation of frcmod of FES in AMBER ?

Hi everyone, I have to do Molecular Dynamics Simulations of a FE2S2 center containing protein. I need to generate the FE2S2.mol2 and FE2S2.frcmod files. I have used the antechamber and parmchk...

11 December 2017 1,826 0 View

Query about FES cluster topology in GROMACS?

Hi everyone, I have run the molecular dynamics of FES cluster containing protein in GROMACS. I got the error that FE and FES are not found in the amino acid database of force field. What can i...

10 November 2017 9,793 0 View

Occupancy of hydrogen bonding in VMD after molecular dynamics ?

Hi everyone, I have done molecular dynamics simulation of protein with ligand in GROMACS. I am not much aware of occupancy of hydrogen bonds in complexes. What does occupancy of hydrogen bonds...

09 October 2017 2,652 0 View

Hydrogen bonding distribution in molecular dynamics simulation in gromacs?

08 September 2017 852 0 View

Error in MD by gromacs

06 July 2017 8,975 0 View

Consideration of one chain or two chains in MD by Gromacs

Hi all, I have to do molecular dynamics of a protein. it is trimer of dimer. It has total 6 chains Although in dimer both chains have same amino acids. It has 6 ligands. Ligand interact via...

06 July 2017 6,005 6 View

Dear all, I was wondering if anyone knows whether MGLtools and Autodock can run on Mac OS?

I have tried to download the 64-bit version of MGLtools however, as many times as I have downloaded and uninstall the programs, an error arises that the app needs to be updated. Thank you.

03 March 2021 5,997 2 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

I got 02 moderator values defining Johnson-Neyman significance regions. Is it an error?

Hi everyone, I am conducting research for my Master's thesis. I am using PROCESS by Johnson-Neyman to analyze my Moderator model. I test the relationship between Public Service Motivation and...

03 March 2021 2,350 2 View

Do I need to do linear regression before running mediation analysis using PROCESS MACRO by Hayes ?

I just wanted to check if I need to run a linear regression separately if I am using PROCESS MACRO to run mediation analysis. Thank you.

02 March 2021 4,359 3 View

Do I need to strip the PVDF membrane before staining it with colloidal gold?

Dear Colleagues, After running Western blot on PVDF membrane and detection using ECL, I would like to stain my PVDF with colloidal gold to be able to allign the ECL image with total proteins on...

02 March 2021 7,829 3 View

PACYC PCR not working after several attempts. Would anyone have any suggestions?

So, I have been trying to run a pACYC PCR which will be used later on for a Gibson Assembly. However the PCR is not working. I have already tried gradient PCR and changing extension time; however...

02 March 2021 1,146 2 View

What SPSS analysis should I run with one IV (with two levels) and two DVs?

Hi, I am trying to figure out which test would be most appropriate to run for the following question: Is there a difference in task blood pressure between smokers and non-smokers? There are two...

01 March 2021 8,235 2 View

OpenBCI eeg--has anyone used them?

I'm looking to try out an off-the-shelf EEG set for some exploratory work. Curious if anyone has used the OpenBCI, and how much set-up work is required. I've heard they are more difficult to get...

01 March 2021 4,128 3 View

Is there any expert in Smart PLS who can help me?

Dear colleagues, I have a manuscript that needs an expert in smart PLS to run the analysis, Is there anyone expert and ready to help me, please?

01 March 2021 8,212 3 View

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...

28 February 2021 5,650 1 View