Can I use discovery studio for simulating a compound docked with a human protein target using Glide-IFD docking?

Can I use discovery studio for simulating the complex? As glide uses OPLS2005 force field and discovery studio uses Charmm force field, will it be a logical step or not?

08 September 2013 5,171 2 View

MODELLER DOUBTS

Hi all , I installed modeller9v8 in my PC. the command page opens. but when i type as " sequence.ali", i get the following command: " 'sequence.ali' is not recognised as an internal or external...

02 March 2011 1,566 5 View

Kindly help

I am asked to look for sequence similarity and identity for a target protein which is of 120 amino acids. But I have to compare this target with a database of 1500 sequences. so i do not know...

01 February 2011 5,209 2 View

suggestions please

I am asked to look for sequence similarity and identity for a target protein which is of 120 amino acids. But I have to compare this target with a database of 1500 sequences. so i do not know...

01 February 2011 9,226 2 View

RMSD & TM

Hi all, When I work with online servers for my protein, i get an RMSD value of -1 and TM score of -1. What does these values suggest of my protein? can any one of you...

31 December 2010 6,974 2 View

FASTA

Hi, I have a sequence ( human -target)) of 600 aminoacids long. (No structure is available.). similarly i found a sequence(template) in monkey which is the same 600 amino acids long. when both...

11 December 2010 6,720 1 View

OBEJCTIVE TYPE BIOINFORMATICS BOOK- FIRST OF ITS KIND

Hi all I have published a book on 'OBJECTIVE TYPE BIOINFORMATICS" very useful for students who study for various entrance examinations. The cost of the book is Rs.200. 5% discount can be given....

11 December 2010 2,081 1 View

rosetta

Hi can anyone teach me how to work on ROSETTA 3.1? my mail : [email protected]. please send me the steps to work with rosetta

11 December 2010 5,736 1 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

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