How would I get the converged free energy profile for an open-closed transition in an enzyme?

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

Can anyone help with distance constraints in RB dihedral type in amber99sb-ildn ffbonded.itp?

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

Could anyone suggest a suitable software/server where I can model few missing loops in my protein?

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

Are CGenFF parameters (from ParamChem) for peptide analogues good enough to couple with Charmm36 parameters for the lipids in a membrane?

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

Is it possible to assign a particular charge (restraint) on an atom during RESP calculation using REDTools?

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

Is anyone familiar with the B-factor from X-ray structure and simulation comparison?

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

Could anyone please elaborate 'projections of trajectory onto first two principal components' in PC analysis?

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

Why does 5' Phosphate come out of binding pocket during equilibration?

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

Could any one help me in generating a residue-residue contact map?

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

How difficult is to close a loop of a protein by reinserting ligands inside the active site?

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

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MGL tools

20 June 2021 0 0 View

fatal error

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

fatal error

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

fatal error

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

fatal error

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

flexibility of polymers chain

effect of double bond on the flexibility of polymers

07 April 2021 0 0 View