Has anyone performed any kind of QM/MM simulations in gromacs-4.5.5, and in latest version of CMPD?
I am studying an enzyme where the closing of a loop should happen upon ligand binding to the active site. In unbiased simulations, even after 300 ns of simulation time the loop does not close the...
05 June 2016 6,370 12 View
Dear All, I need to impose a distance restraints between COM of protein active site residues and COM of a ligand. But the problem is I am using an .itp file generated from acpype. While I use the...
06 July 2015 4,937 0 View
I would like to model three missing loops in a protein. Unfortunately, there is no similar protein having these missing residues (template is not available). I tried to use FALC-Loop server, but...
04 May 2015 2,546 11 View
I need a suggestion related to simulation of peptide-membrane system. I've got tentative CGenFF parameters for the peptide analogues from ParamChem with charge and param penalties 35 and 53...
01 February 2015 8,417 1 View
I'm trying to calculate RESP charges of atoms in a complex system. I need to keep a fixed charge on certain atoms during the charge calculation. Is there any such procedure in REDtools or REDserver?
31 December 2014 10,126 4 View
I am getting a B-factor difference of ~250 A^2 between X-ray structure and simulation (8pi2 msf/3), plot is attached. The overall trend is in good agreement with the crystal structure. Generally,...
11 December 2014 637 13 View
Projection of trajectory onto first two eigenvectors- Does it mean that i) the superposition of molecular structures (a set of C-alpha coordinates) over a trajectory are projected onto a plane...
11 December 2014 4,618 2 View
I need to generate a residue-residue contact plot for a protein. I was trying in VMD but there I didn't find a way improve the quality of the plot, I mean a way to include the residue indices,...
10 November 2014 9,184 5 View
While simulating a protein-ligand complex, during equilibration the 5'-phosphate group of it is coming out of its binding pocket. Few water molecules are crawling in. I have performed two...
10 November 2014 3,369 10 View
I see a flexible loop opening from a protein after removal of the ligands from the active site (Molecular Dynamics simulations). I expect that the reinsertion of the same ligand molecules in the...
07 August 2014 6,364 3 View
Hi, I'm currently working on a project where I need to plot the atom-projected band structure using GPAW. I've been able to calculate the band structure for my material, but I'm having trouble...
07 August 2024 269 3 View
Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...
06 August 2024 1,495 2 View
kindly reply me. Thanking you in advance.
05 August 2024 7,727 4 View
Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...
03 August 2024 3,371 3 View
I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?
02 August 2024 3,143 4 View
Molecular docking software/ websites?
02 August 2024 8,704 7 View
Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out? For example consider a process for certain product manufacture where a new process flow...
31 July 2024 781 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, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...
29 July 2024 1,092 2 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