During simulation of glucose O5 atom and anomeric OH group are getting attached together.what could be possible reason?how important is charge?

I am facing a problem in (0GA+ROH) GLYCAM carbohydrate parameter while doing force field preparation for glucose molecule in AMBER. I have used Gaussian optimized structure and calculated the MK...

10 November 2017 3,045 0 View

How can calculate resp charge?

I want to know how calculate the resp charge. I have followed the tutorial for understanding of resp charges in amber 16. For calculating the charge i have used only "linker part"...

10 November 2017 4,040 1 View

How can i plot graph in xmgrace?

I have two different set of graph one set is starting from 0-200 and one set is 0-200 on x-axis. how can i merge both sets in xmgrace so that the total graph should be 0-400. means the x axis has...

10 November 2017 1,664 1 View

Why serine amino acid is behaving like a positive entity in protein electropotential surface?

I have serine aa in the core of protein behaving as a positive entity which i inferred from electropotential surface. as it contain OH negative its should behave as negative entity. I am not able...

09 October 2017 8,375 1 View

How can set a parameter for Ag+ ions in AMBER16?

31 December 2016 7,626 4 View

What is the meaning of EPW in water box ?

When I solvate the protein in AMBER16. EPW H2O shown in (AMBER output file) solvated PDB file.I don't understand what is the meaning of EPW. I have attached screenshot. kindly let me know.

31 December 2016 5,528 0 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

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

How the parameters (such as Mw, Chemical bonds, polymer bland and so on) affect the mechanic property of polymer (such as storage, loss modulus) ?

Anyone can recommend any books on such topics? Thanks in advance.

02 March 2021 8,457 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

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

How can you bring two structures together to create an adhesive bond in LAMMPS?

I have created an Ice 1h crystalline structure and an Aluminium substrate structure and equilibrated both at 250K. Now I need to bring them together in a way that an adhesive bond is created....

01 March 2021 3,325 2 View