How to estimate hydrophobic interactions and electrostatic interactions between the protein chains using GROMACS?

Dear GMX experts, A simulation system consists of several peptide chains, and I would like to compare contacts of hydrophobic and electrostatic interaction. How can I estimate hydrophobic...

03 April 2018 9,735 3 View

How to convert CHARMM .str to .itp file for GROMACS?

Dear Experts, I generated LIG.str file using CGenFF for a specific molecule. I would like to use GROMACS package. I tried to convert LIG.str file to LIG.itp file. I tried as following command...

31 December 2017 9,258 3 View

How can I know the structure was optimized or not?

Hello, I am very new user of Gaussian. I started the optimization of the connected two amino acids. Calculation was finished, and I would like to get the optimized structure. How can I know...

05 June 2017 7,037 5 View

Which protein structure viewer useful for draw vectors?

01 February 2016 3,326 1 View

Can someone verify my singular value decomposition of 3D helical data?

01 February 2016 8,378 0 View

How do I make a pH dependent simulation of Oligomer structures?

Hello, I want to make pH dependent simulation of dimer, trimer and pentamer structure of peptide. How to make it using AMBER or GROMACS? Can I use H++ server for oligomers? or How to set manually....

31 December 2015 769 2 View

How to fix malloc error during MM-PBSA calculation on AMBER14

Hello, I have got following error during MMPBSA.py calculation for PBSA MD simulation. How to fix it? ******************************************************************** Beginning GB calculations...

10 November 2015 10,029 2 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

New Journal, "Integrative Psychological and Behavioral Science" -- do you not know, and have you not seen, this done before?

Question to you and THEM, the New Journal, "Integrative Psychological and Behavioral Science" -- do you not know, and have you not seen, this done before? There appears to be a core problem for...

02 March 2021 3,024 2 View

Can we distinguish the type of free fluid inside the pelvic and abdominal cavities whether blood or serous fluid using the ultrasound?

during ultrasound examination of acute abdomen, sometimes we see free fluid , can we know the type of fluid ,whether blood or not , using ultrasound only? if yes , what are the sonographic...

01 March 2021 7,476 4 View

Does any one can help me choose a reasonable basis set for intermediate metal ions interactions with guanine (i.e Fe2+, Mn2+, Cu2+ and exc.)?

Hello every body Does any one has any idea to help me choose a reasonable basis set for intermediate metal ions (i.e Fe2+, Mn2+, Cu2+ and exc.) interactions with guanine or other DNA organic...

01 March 2021 6,187 2 View

What could be some reasons why unstimulated monocytes are getting activated?

Im doing PBMC isolation -> CD14+ enrichment using magnetic beads -> stimulation setup. My negative control is just cells in cRPMI but they seem to get activated over and over again.

28 February 2021 7,883 3 View

Can anyone help me with the administration of the "Mind the Gap" Scale for satisfaction with transition to adult care?

We are working on a study focused on adolescents' transition to adult care and are looking for a validated measure for satisfaction with the transition. So far the only measure that we have came...

28 February 2021 2,338 1 View

Why does intensity drops as concentration increases?

Is there any reason for decrease in fluorescence emission intensity of HSA,BSA when increase the concentration ?

28 February 2021 3,653 4 View

POlymer+DMSO solution and moisture??

What could be the reason of moisture at the sides of Vial when I am preparing my polmyer+DMSO solution for membrane fabrication? What etiquettes I am possibly missing here?

28 February 2021 6,516 5 View

Should we reduce the standard unit of length to 0.31951540592 meter ?

The reasoning behind this question is to align the ratios of the proton potential in energy per charge to the speed of light in distance per time. As these two dimensions appear to be related,...

27 February 2021 947 7 View

How to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...

27 February 2021 4,703 1 View