How can I find the rise per residue in a protein?

More Prasun Kumar's questions See All

Monitoring Thermal Denaturation

06 July 2017 7,494 0 View

G-Helix and number of residues in a helix ?

02 March 2017 1,856 1 View

How do I calculate the angle between two vectors in 3D space using atan2?

I have two vectors in 3D space and I want the angle to be in -pi,pi. Hence intend to use atan2 in place of acos function. It will be a great help, if some body can guide me.

01 February 2017 3,830 3 View

Can someone please help with Clustering 2D dataset?

I have a matrix consisting of 10000 rows and 2 columns. I wanted to cluster my dataset into k number of clusters. I am aware of the K-mean available in MATLAB, but its clustering is based on first...

04 May 2014 660 4 View

Can anyone help with small molecules and their superposition?

I have two small molecules and want to superpose them on each other. Can somebody suggest me some command line program (Linux)?

03 April 2014 2,407 10 View

Can someone help me with my simulation of Fe2+ ions and protein?

Hi all, I have to run a simulation using GROMACS, which has Fe2+ ions. In GROMACS, the C12 and C6 values for Fe are not defined. Can anybody help me in this regard? Any article or relevant data...

02 March 2014 6,453 10 View

Is there any software available to identify the central strands and end strands of a beta sheet?

Is there any software available to identify the central strands and end strands of a beta sheet or to identify the parallel and anti-parallel beta sheets?

07 August 2013 8,128 2 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

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

i have some problem with chtMultiRegionSimpleFoam

--> FOAM FATAL ERROR: Maximum number of iterations exceeded From function Foam::scalar Foam::species::thermo::T(Foam::scalar, Foam::scalar, Foam::scalar, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar) const) const [with Thermo = Foam::hConstThermo >; Type = Foam::sensibleEnthalpy; Foam::scalar = double; Foam::species::thermo = Foam::species::thermo >, Foam::sensibleEnthalpy>] in file /home/ubuntu/OpenFOAM/OpenFOAM-4.1/src/thermophysicalModels/specie/lnInclude/thermoI.H at line 66. FOAM aborting #0 Foam::error::printStack(Foam::Ostream&) at ??:? #1 Foam::error::abort() at ??:? #2 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::calculate() at ??:? #3 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::correct() at ??:? #4 ? at ??:? #5 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" #6 ? at ??:?

24 March 2021 0 0 View

Conrado Pedebos

I believe that the g_helix tool from the GROMACS simulation suite is able to do that, as long as you have a .pdb file.

Prasun Kumar

Thanx for the reply.......For the helix even HELANAL-Plus does the correct calculation, but the real problem arises when the segment is strand (though strand is considered as helix) or loop.....Any suggestion for this........