Using tLEaP to generate Amber prmtop file?

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I need content writers, poets, researchers to my new online magazine, would you be interested?

Good day! I am the CEO of an online magazine called Order Of The Pen . We specialize in promoting new writers via our platform on Wix and Partnership with Mailchimp for email marketing,...

18 June 2024 4,117 0 View

I want to do research on business related issue.Do you have any idea what topic i should choose?

its about my masters dissertation

10 June 2024 5,490 7 View

Is something wrong with my setup that I cannot elicit a response from field EPSP?

Hi all, I have been attempting to do field EPSP but I am not able to elicit a response. I am using a thin walled electrode for the recording electrode at 1.5mOhm resistance. I have filled the...

10 June 2024 2,418 0 View

What is the best extraction method of sulfonamides group from honey samples?

What is the best extraction method of sulfonamides group from honey samples? during the testing of the same sample over a period of a time we noticed that concentration of sulfonamides drugs...

09 June 2024 8,184 2 View

How to address the challenge of combining force field parameters?

I have generated force field parameters for solvents using AmberTools and adopted force field parameters for a lithium salt from a published paper. How can I effectively combine these two sets of...

03 June 2024 6,892 0 View

Can HCl be used instead of H2SO4 for RNA later preparation?

I am preparing RNA later following the patented protocol. It is mentioned there and in other recipes as well to use H2SO4 to balance the pH to 5.2. If H2SO4 is not available, can I use HCL instead...

30 May 2024 3,220 0 View

How to calculate variation on qualitative variables ?

I am using IBM SPSS version 21 as a statistical analysis software. My research is about comparing 2 diferent populations. Let's say it's group A and group B. Each group has variables changing...

15 April 2024 692 13 View

How to generate LT files?

I am working on liquid electrolytes. I generated GAFF parameters by using AmberTools. Now, I am trying to create LT files from Moltemplate. I am discussing my issue here in the hope that someone...

02 April 2024 7,067 0 View

Simulation of solvation structure of electrolytes using LAMMPS?

Hi, I aim to conduct MD simulations using LAMMPs. I am trying to convert MOL2 and FRCMOD files into the moltemplate file format (LT). Initially, I generated LT files for my molecules, but I am...

19 March 2024 6,192 0 View

How to make a protein soluble?

My expressed protein is being collected in the pellet fraction and I have used different strategies for making it soluble but still its coming in the pellet. I have used strategies like...

19 February 2024 5,552 0 View

1. If I can quantize the atom using this hyperbolic spiral and classical physics, could nature do the same?

If we map as a continuous motion an ionising electron (beginning its journey at n=1) in an H atom, a specific hyperbolic spiral appears (see animation). When we solve this spiral formula, we find...

07 August 2024 5,343 2 View

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 1 View

Should I include H atom into C3N5 when i am doing DFT modelling?

Hi all, my experimental XPS results shown that my C3N5 sample consists of N-H bond, hence in this case I should incorporate the N-H bond into my DFT modelling. However, I do notice several papers...

07 August 2024 8,414 2 View

Why reactivity isn't increased with more empty spots in valence shell?

If from a geometric perspective the non-halogens, non-noble gases have more empty spots in their valence shell, and the filling/exiting of any of the empty spots in the shell constitutes a...

03 August 2024 4,787 2 View

Why do paired electrons atoms produce no magnetic field lines?

If you think of electrons with spin as bar magnets, you know bar magnets of opposite polarity as long as they're not occupying the same spatial location don't cancel out each other's magnetic...

03 August 2024 3,927 2 View

How can you draw a coordinate bond between a metal and donor atom in metal complexes, using discovery studio visulizer software?

Hello,, The metal complex ligand appears incomplete in the screen of the discovery studio visualizer

30 July 2024 3,354 1 View

How to do pca analysis of c-alpha atom of the protein?

i m interested in pca analysis of c-alpha atoms in gromacs for that i used the following gmx_mpi covar -s mdca.tpr -f mdca.xtc -o eigenvalca.xvg -v eigenvecca.trr -av average.pdb -n index.ndx but...

30 July 2024 1,607 1 View

Why am I observing very high Temperature and Pressure Increase using NPT Ensemble?

Hello everyone, I am running DFT with CP2K software at 1200 K, 1 bar with a periodic system of 64 Al atoms + 2 CO2 atoms. However, I am seeing my temperature slowly increase to >4000 K and my...

22 July 2024 3,177 0 View

How to create parameter and coordinate files for ligand in amber when FATAL error (maybe due to duplicate bond specifications) happens?

Hello, I'm trying to create parameter and coordinate files for a drug (PRG-A01) found on the following page: http://www.probechem.com/products_PRG-A01.html I used the guide made by Michael...

17 July 2024 3,472 3 View

Why Cl atom is not showing in docked comlex of molecule?

During the preparation of a ligand molecule in autodock or openbabel Cl atom is not showing in the .pdbqt file whereas it was present in the pdb and sdf file. Due to this Cl atom is not showing in...

13 July 2024 3,486 6 View