How do I decide about the autodock binding energy and R-S-face of ligand?

I am working with Short chain Alcohol dehydrogenase(R-ADH) for converting ketones to alcohols. The reaction mechanism is that the enzyme accepts the ligand, such that its S-face faces towards the...

02 March 2015 3,441 7 View

Can anyone help with a query related modeller?

I have a template 1ZK4 and query R-ADH of brevis. I was able to do modelling using modeller with cofactor NADP. But when i tried to add water I observe that the alignment between template and...

04 May 2014 6,707 4 View

Query related to Modeller 9.13- Can anyone help?

I don't have any idea about Python programming and i have recently started using Modeller. I have used the scripts that are present on the modeller site. I am able to successfully run the first...

03 April 2014 4,206 5 View

Can anyone help with PyMol?

I have docked structure, different conformations from autodock, but I am not able to get how to visualize those docked structure in PyMol. Since many literature mention this but am unable to do so...

02 March 2014 4,681 6 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

flexibility of polymers chain

effect of double bond on the flexibility of polymers

07 April 2021 0 0 View