Can anybody suggest a tool to identify co-ordination bond and hydrophobic interactions influenced by metal ions?

I have modeled a protein and ligand complex with divalent metal ions. I want to find various types of interactions influenced by metal ions. I used ligplot..but it is showing only co-ordination...

10 November 2013 6,490 3 View

How to identify potential target protein of any novel small compound in target fishing?

I have synthesized some small molecule. I searched in PubChem, there is no similar structure found in Pubchem database. How to identify the potential drug target for the newly synthesized small...

06 July 2013 1,488 7 View

Does any one knows how to do do_dssp in gromacs?

I copied dssp executible from http://swift.cmbi.ru.nl/gv/dssp/HTML/distrib.html and saved in /usr/local/bin/dssp folder. and run the command /do_dssp -f ions2.trr -s ions2.tpr -na -o dssp.xpm i...

31 December 2012 4,786 2 View

How to do do_dssp in Gromacs4.5

I have downloaded dssp.exe file from http://swift.cmbi.kun.nl/gv/dssp/ and bopied in my /usr/local/bin folder. and trying to run command do_dssp protein.xtc -s protein.tpr -o protein.xvg I am...

09 October 2012 9,588 12 View

What can I do with purified proteins?

I have purified one membrane protein for protein crystallization. I am refining the conditions for crystal. What else can I do with this purified protein? I am searching for some new approaches or...

09 October 2012 9,848 19 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