Can a protein model, i.e. designed using abintio method, be used as a template for the same sequence in modeller to obtain better refined structure?

More Raja shekar Varma Kadumuri's questions See All

Suitable expression system for 30-40 residue peptide His tag or GST ?

Hi, I would like to express and purify a peptide of 30-40 residue long. I would like to know if I can use pET-31b vector with HIS tag or should I go with pGS-21a with GST tag. It would be helpful...

11 December 2014 897 5 View

Is it possible to correlate stability difference between different peptides by doing unfolding MD simulation at 400K?

08 September 2013 4,575 7 View

Is there any script or software available to calculate distance between End C-alpha (C-alpha end to end distance) in a peptide sequence?

I would like to calculate distance between end c-alpha atoms in some peptide sequences, I'm trying to accomplish this task by writing some perl scripts but i'm facing some errors in my script so...

07 August 2012 8,842 6 View

How to upload multiple pdb files in jmol applet, and execute scripts on required pdb file ?

Is there any method to upload multiple pdb files in jmol applet, and execute scripts on required pdb files..

07 August 2012 469 1 View

I want to super impose my loop structures based on the topology ?

I want to super impose my loop structures based on the topology, so i would like to download cora suite,but i am not able to find it anywhere pls help me if any one has info regarding cora suite...

01 February 2012 9,366 1 View

Can any one tell me how to get PROFASI software,and also is there any other alternate softwares to it.............

31 December 2011 1,329 0 View

Hi, can any one tell me what are the best softwares (online/downloadable) for checking stability and activity of a designed protein.

I want to check stability and activity of my designed protein can any one help me by giving info regarding what are the best softwares that are available

11 December 2011 4,013 3 View

Hi, i want to check the stability of my designed protein in which i've replaced a 5residue beta/alpha loop can any one tell me the process or any tool...

Hi, i want to check the stability of my designed protein in which i've replaced a 5residue beta/alpha loop can any one tell me the process or any tools available.........

11 December 2011 8,484 7 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

Luis Morales-Quintana

It depends what the purpose of obtaining this model, since such tools is limited to the type of concluciones you want to get the model.

Nutan Chauhan

Dear Raja Sekhar

can you please provide the link of that paper who used predicted model of protein as a template?

Will be great help.

thnx