I want to perform a free energy calculation on a dihedral, rotating from zero to +pi not -pi to +pi.
I am using plumed + gromacs for my calculation. Can anybody suggest how to put this colvar limit?
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 6,256 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 4,818 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 2,303 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 8,302 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 10,003 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 537 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 4,494 2 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 3,250 10 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 9,049 5 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 6,254 3 View
How to calculate the RMSD values for a MD simulation using MOE?
07 August 2021 0 0 View
When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.
16 June 2021 0 0 View
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
Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...
03 March 2021 5,978 5 View
Hi, I am after the reference below, my library says it cannot obtain a copy either locally or internationally, any help appreciated! Chris Wang ZM, Heshka S, Wielopolski L, Pi-Sunyer FX, Pierson...
03 March 2021 6,193 1 View
Hi, Could you help me to get the latest (2019, 2020) solar resource data for a particular site in JAPAN? PV GIS and NSRDB data are not in reach to JAPAN, I'm looking for some other database for...
03 March 2021 961 3 View