I want to study the role of different structural factors which helps in stability and activity of Enzyme in different habitat. they have basic level of similarity in amino acids sequence (40%)
I guess you can try to follow GROMACS tutorial. Maybe doing the equilabration phase using simulated annealing.
Because many scientist groups are working on this problem. Success rate at laboratory level had been reported but at field level hardly we will find any story.
10 November 2017 9,090 0 View
I have a .pdb file, in this file when I want to use pdb2gmx command> there is this error massage:> Fatal error:> Incomplete ring in HIS680Ask What should to do?
06 July 2015 5,225 12 View
During add ions steps using Gromacs the overall charge on my protein was calculated qtot -35 So i have to add positive ions to neutralize the charge on protein. then i have added 35 Na ions using...
06 July 2015 4,637 3 View
During MD simulations i got fatal error during energy minimization step after commend: gmx grompp -f minim.mdp -c 2HQA_modified_solv_ions.gro -p topol.top -o em.tpr Fatal error:number of...
06 July 2015 2,032 2 View
During MD simulations i got fatal error during energy minimization step after commend: gmx grompp -f minim.mdp -c 2HQA_modified_solv_ions.gro -p topol.top -o em.tpr Fatal error:Too many warnings...
06 July 2015 6,137 4 View
i wanted to determine molecular dynamics of a protein at different temperature.
06 July 2015 4,253 3 View
I used gene specific primer to amplified the gene which is almost 4000 kb in length but i got smear on gel after trying the Mgcl2 gradient and Tm gradient. I got smear with Mgcl2 conc= 3.5,...
07 August 2014 2,263 8 View
Computational approach
11 December 2013 9,927 2 View
I am just starting work on xylanase. Can you suggest an appropriate site for sample collection of xylanase?
05 June 2012 2,593 6 View
I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?
11 August 2024 5,138 1 View
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
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 aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...
05 August 2024 6,787 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
I am attempting to conjugate PEG to an amino acid at the C-terminus, for the purposes of producing nanoparticles. I have been told that PEG modified with amine groups can be used for this purpose,...
31 July 2024 2,033 1 View
I am currently working on a project involving liposomes and need to determine the maximum volume of siRNA that can be added to a 2.5 mL liposome solution with a total lipid concentration of 10...
30 July 2024 6,420 1 View
Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar
29 July 2024 3,084 8 View
I want to do 2,3-butanediol dehydrogenase(BDH) enzyme purification to confirm its activity for 2,3-butanediol. Before that, I need to confirm which N or C terminal tagging is better for enzyme...
28 July 2024 366 3 View