1] I want to solvate a protein with ammonia , how can i do it? Is there ammonia .gro/ammonia.pdb file available.?
2] How can i solvate with a mixture of solvents > eg., ammonia and water...??
You have to create a topology file (***.itp) for ammonia and a ***.pdb file containing single ammonia.
In your ***.top file write
#include ***.itp.
Then, use genbox /gmx solvate command with -ci and -nmol flags to insert required number of ammonia molecules.
Hello, I have run a simulation of amino-acid +water system in GROMACS software. Now i need to get the water orientation profile (ie., how the water molecules are oriented w.r.t specific...
11 December 2017 4,485 4 View
Hello, I have ran a energy minimization, followed by nvt, followed by md run. My md run mdp (ie., md.mdp) has dt = 0.002, nsteps = 30000000 ; [0.002 * 30000000 = 60000 ps (60 ns)]nstxout = 5000 ;...
04 May 2017 2,588 2 View
Hello,I want to calculate RDF of glycine of Hn-OW, Hn-HW, Ha-OW, Ha-HW, Ca-OW, etc.,So my commands were as follows... 1] To make indexes:- gmx make_ndx -f md.gro -o Hn-OW.ndx > del 2 Removed...
02 March 2017 4,935 1 View
Approximate concentrations are require in compared with the WHO permissible limts
11 August 2024 2,723 1 View
Hey there, As a synthetic chemist delving into theoretical calculations for my imidazolium-based organic molecules, I would greatly appreciate any guidance on the appropriate input instructions...
09 August 2024 5,444 7 View
I'm currently working on calculating the collision cross section (CCS) for various ions, and I'm facing challenges when dealing with sodiated and multiply charged ions. Most of the resources I’ve...
08 August 2024 8,329 0 View
Hello What should be done to separate and identify organic acids in HPC when their RetTime is the same?Like oxalic acid with Propanoic Acid.or acids that have a very close RetTime.
07 August 2024 8,782 3 View
Palmitic acid presence in aqueous fraction
05 August 2024 8,624 4 View
I used humic acid at 0.044 g/kg soil in my pot experiment. But finally, I have to recommend kg/ha. Each pot's soil weight was 11 kg. What is the solution?
02 August 2024 7,186 6 View
Hello! I have this scale which had 10 items initially. I had to remove items 8 and 10 because they correlated negatively with the scale, and then I removed item 9 because Cronbach's alpha and...
01 August 2024 4,606 7 View
Just bounced on me. Before statistically analysing significant difference, shouldn't we see if data fits normal distribution first? Is 3 replicates enough to testify the hypothesis of normal...
31 July 2024 8,141 13 View
Does anyone know of a module for the JAMOVI software that is capable of generating mean separations using the classic letters based on post hoc results (e.g., Tukey test)? If, as I believe, such...
31 July 2024 3,333 4 View
Hi everyone, I'd like to better separate two close peaks coming from a bioconversion sample, I'm currently using a C18 KromaPhase 4,6mm Ø.I. SCHARLAU, particle size (µm): 10, pore size (Å): 100,...
30 July 2024 435 3 View