How to solve the problem "RESTARTED DUE to LINMIN FAILURE"?

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Statistical Tests for Quantitative Study?

Hello Everyone, I have one population, sample size 200. and needed to find the correlation between Variable A and B. Also, which T-test should I choose for hypothesis testing Please advise...

21 February 2021 7,591 4 View

Is there any specific software available for graphical presentation of signaling pathways/cycle in cells?

I'm planning to write a Review article, to make it more worthy and easy to understand for the targeted audience, I'm thinking to add some signalling pathways, and unfortunately, I have no idea how...

30 December 2020 6,395 2 View

What are the models of artificial intelligence based cars in automobile industry scientists are working currently with sustainable approach?

The question also includes the assurance of safety in the self-driving cars and the expected cost of selling. And what kind of quantum model will be more suitable in terms of physical realization?

29 October 2020 5,352 3 View

Want to Implement Watermark on Steganography Image?

I want to implement steganography to image to hide data and then implement watermarking algorithm to ensure the owner. Someone suggest me to use cloudsim software. Is it possible to implement this...

05 October 2020 2,750 4 View

How to calculate the activity of a catalyst in mol/kg/hr?

Hi all, I have done a CO oxidation reaction by using Palladium impregnated activated carbon based catalysts. The catalyst was showing the 100% conversion for a duration of 3-5 hrs. How can I...

28 September 2020 997 2 View

Can anyone help me out to find out my masters thesis research topic??

My area is software engineering, I haven't any idea about the thesis. need lots of help. I want that the topic should be Lil bit easy. :P Thank You

06 September 2020 4,678 14 View

How can you prepare rats synovium of knee joint for histopathology, H and E and special stains?

Tissue processing techniques in particular..

06 September 2020 5,701 3 View

For how many days a human can survive in Subtropical Broad-leaved Hill Forests with 500 calories of veg and how?

Subtropical Broad-leaved Hill Forests such as Assam sub-tropical hill savannah woodland in India has a wide range of vegetation and is home to thousands of kinds of herbivores. What if a human has...

27 July 2020 2,350 7 View

Validated Survey Instrument?

Hi, I am a PhD student and in my dissertation I have to conduct a survey for my quantitative research. My professor wants me to use validated survey instrument. I wanted to use Question Pro...

26 July 2020 559 7 View

IS it Necessary for Primers in Taq-Man PCR to be HPLC Purified?

I want to set up a taq man reaction. I want to know that in taq man reaction I have to order HPLC purified Primers or ordinary primers are adequate for me. If you have experience in taq man,...

23 June 2020 5,511 3 View

Does AMBER or CHARMM force field parameters have coarsed grained side chain parameters?

I need to coarse grain the side chain with a single atom. However, what force field parameters do I have to use. Does AMBER or CHARMM have any parameters and partial charges for coarse-grained...

31 January 2021 7,091 3 View

The lipid bilayer broken down and form micelle within 1ns MD simulation. How to simulate lipid bilayer without breaking bilayer?

To simulate the lipid bilayer (10-10, 25-25 so on) from CHARMM-GUI membrane builder, we used to simulate it at various force field (AMBER14, AMBER03, AMBER14IPQ, AMBER15FB, NOVA, YAMBER) at water...

26 January 2021 7,816 2 View

AMBER tleap solvatebox always undervalues the density, why?

I've been searching for an answer to this question for years, and I'm shocked I haven't found any discussion on any forums. Here is an example to provide more details: I am preparing a 450...

20 January 2021 7,561 2 View

Can i use MM-PBSA to calculate the binding energy of a glycan ligand? ad how?

I have a protein-ligand (glycan) complex and want to do an MM-PBSA analysis using AMBERTOOLS after doing MDS (NAMD). What are the files necessary I should prepare for glycan? Note: I used...

30 December 2020 2,658 2 View

Is there anyone who can help me parameterizing theligand molecule with AMOEBA polarizing force field for using it in AMBER?

I am able to generate the parameter topology files for protein and water box using TINKER but am not able to generate these for my ligand as it is finding no atom types and atom class in TINKER....

17 December 2020 4,309 1 View

Any Molecular Dynamics Tutorial for Membrane-Bound Proteins in Amber?

Hi everyone I'm currently working with a membrane transporter protein to which I need to simulate molecular dynamics (MD). For this, I have inserted my protein in a membrane with CHARMM-GUI and...

16 December 2020 407 1 View

How to Convert GAFF ff in Amber to Input Files in Gromacs?

Hi users, I found the topology files for choline with GAFF ff in literature (coa.ff and colinab3lyp08.prepi.txt) and I would like to convert these file to the input files I can use in Gromacs....

20 October 2020 4,288 3 View

Parameters for magnesium acetate in AMBER MD simulation?

I am trying to use Magnesium acetate [Mg(CH3COO)2] as the salt instead of Sodium chloride [NaCl] in my tleap. Are there any AMBER parameters for acetate ion that I can use?

12 October 2020 931 3 View

What is the alternative for G_MMPBSA for latest versions (After v5.1.~) of GROMACS?

Hello Researchers The support for g_mmpbsa is not extended for the latest versions of gromacs (2020). I have already performed 200ns simulations and wish to perform PBSA calculations. What could...

28 September 2020 9,840 2 View

Does any one can help to calculate viscosity using molecular dynamics. I am doing the NAMD SIMULATION using amber force field?

My system consists of ionic liquids, aliphatic and aromatic hydrocarbons. Any suggestions and any script for calculation of viscosity?

24 September 2020 6,640 1 View

Yudibeth Sixto-López

Munazzah Fatima Ansari Maybe it is to late to respond to you question but I hope it helps you and others facing the same problem. First of all, I strongly recommend to visually inspect that your model is correct and does not have any atom overlapped or somethins strange after that It could be convenient to increase the NCYC stepts as suggested in this forum. http://ambermd.org/Questions/linmin.html

All the best

Yudibeth

Munazzah Fatima Ansari

Thanks Yudibeth Sixto-López. I did minimization with two step process. First minimize without SHAKE. Afterthat use the SHAKE and minimize. It resolve my problem. But Thanks again for suggestions.