Where I can find tutorials for using AMBER molecular dynamics software on supercomputer?

Hi, I am wondering what are the files that should be prepared? how? commands? that enables me to perform MD simulations using AMBER on Supercomputer.

11 December 2019 5,978 5 View

What database or anything else enable me to find the pharmacological actions of certain pharmacophore?

I want to find a database in which i can draw the chemical structure of the core ring and it will give me all the published structures with their biological activity. For example, the...

05 June 2018 1,191 11 View

How can I get a list of FDA-approved drugs of certain category?

I'm wondering how i can find an updated list of FDA-approved drugs for example, proton pump inhibitors, Topoisomerase inhibitors or whatever category.

04 May 2018 4,914 5 View

Any recommendations for highly viscous solvent but should be non-polar and aprotic one?

I'm wondering if you could suggest highly viscous solvent which is non-polar or slightly polar and can't form H-bond interactions. Most preferrably: a glass forming solvent at low temperatures to...

04 May 2018 3,493 4 View

Where I can find a downloadable list for Quartile (quantile) journals ranking?

I'm also wondering is this ranking standard or it differs from website to another.

02 March 2018 6,806 7 View

Some questions regarding proteins sequence and structural comparison?

I hope you can help in these matters. 1) What is the difference between sequence and structural comparison between proteins? 2) Which website or software is good to use to perform this task? 3)...

10 November 2017 9,633 5 View

What are files required to submit GROMACS job on supercomputer?

08 September 2017 2,553 13 View

Intermolecular H-bond bond can be converted into a covalent bond ?

From scientific point of view, if a h-bond is formed as in RN-H.....NAr The covalently bound proton can transfer to other side forming RN.....HN+Ar if it can take place, is there a reference for...

07 August 2017 9,998 6 View

How to purify BSA (Bovine Serum Albumin) for Absorption/Fluorescence spectroscopy use?

07 August 2017 4,999 3 View

Understanding synchronous fluorescence spectrum?

In Synchronous spectrum, both Exc and Fl monochromators are scanned simultaneously. MY questions are; 1) How to determine delta wavelength 2) if delta wavelength is 20nm, does it mean the data...

06 July 2017 4,018 4 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