Guidance about computational work and publication?

I found a paper regarding the work we wanted to do. The receptor they have used is same as we have decided to target but the ligands are not same, we have our own novel compounds belonging to the...

09 October 2013 260 8 View

Can someone advise on modeling of structure?

I have 2 sequences, I have modeled them by using I-tassar, as homology was so less as 20%, so can't use modeller suite. I have got 5 sequences from I-Tassar, ab-initio modelling, after...

09 October 2013 2,855 7 View

Why is necessary to do simulations after docking, and why is water used as a solvent for simulations?

Simulations after docking

08 September 2013 9,520 11 View

Change of functional groups, affect on docking studies?

I wanted to know, what changes will occur, if a replace or remove of a functional group of ligand at give specific site and put it on other position with that ligand, my ligand have steroids and...

08 September 2013 3,257 3 View

How to label or show position of particlar atom on marvin or chemdraw?

After drawing structure of chemical compound I wanted to show or label the carbon oxygen hydrogen atom, like C1. C2 O5 H3 means a position of a particular atom. How can I do this in marvin sketch...

08 September 2013 7,087 1 View

Is it possible to delete a chain that does not have an active site?

my protein consist of 4 chains, A B C and D, my binding pocket is on 2 chains A AND C , can i delete the B an D for carrying out the docking studies, as my binding pocket lies on A and C chain?

06 July 2013 631 9 View

Can someone advise on a virtual screening problem?

I have a set of 30 chemically similar compounds, i want to do virtual screening, should i start docking studies after drawing their structure or should perform other any other analysis...

06 July 2013 997 7 View

Can someone answer a question about a gromacs results analysis problem?

The MD simulations using gromacs 96 force field was done on a compound obtained after semi-flexible docking and flexible docking. The protein was also simulated in water. Comparing the docking...

05 June 2013 9,664 5 View

How to use g energy command?

I have simulated the protein in water and 2) protein with ligand now I want to check the g energy in gromacs for both system individually and then combine to one plot. How could I do this?

04 May 2013 4,651 7 View

Which gromacs force-field is to be used?

I have simulated the protein-ligand system by using the Gromacs force-field 43a1 after obtaining the docking results for semi-flexible and flexible docking. My ligand is a steroid, and they...

04 May 2013 1,290 5 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