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

overlaps

I have a sequence of 100 amino acids. I want to see the overlapping segments in the sequence by splitting into dipeptides, tripeptides. so how to do this analysis? is there any online tool to do...

01 February 2011 7,075 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

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