Can someone recommend a MD force field for phosphorylated cysteine (3-oxoalanine)?

I would like to do classical MDS of a protein containing phosphorylated cysteine (3-oxoalanine) using GROMACS. Which force field should I use?

07 August 2019 7,344 4 View

Why Gromacs mmpbsa shows 'nan' in energy values?

I have performed simulation using gromacs. The protein is of two chains, I am trying to understand the changes in mmpbsa values between the two chains but I get following. What could be possible...

02 March 2019 1,935 3 View

Is it possible to create gromacs ndx file of two chains as a single index file?

I have performed a protein-protein simulation. I wish to see the change in binding between protein chain A & chain B. How to create a index files of chain A & B and do the analysis? Like GROUP 1 :...

02 March 2019 6,250 4 View

Can GROMACS perform molecular dynamics with different pH? If NO, what could be an easiest alternative?

I wish to study the change in interaction of the small molecule with the protein in respective to change in pH. GROMACS focuses most on protonation state and not directly on pH. So how can I...

01 February 2019 3,095 5 View

How to get the nano-particles of different shapes in 3D PDB?

We have identified nano particles of different shapes (eg Ag NPs in rod shape, round, etc.). we wish to have computational study. Is it possible to draw the structures of nano particles or get...

03 April 2018 3,981 0 View

Is it possible to draw the nano particles using software? If yes, what are they?

We have identified nano particles of different shapes (eg Ag NPs in rod shape, round, etc.). we wish to have computational study. Is it possible to draw the structures of nano particles or get...

02 March 2018 7,111 1 View

Could someone suggest a tool to find druglikeness of multiple compounds at a time (.sdf)?

05 June 2017 8,517 0 View

Why many of the drugs in market do not satisfy lipinski rule?

05 June 2017 2,142 5 View

What are the set of parameters and its normal value used in "Quantitative Estimate of Drug-likeness (QED)" predictions?

05 June 2017 7,745 0 View

When considering molecular dynamics simulation, which is more appropriate? A long run dynamics or multiple run dynamics?

03 April 2017 2,597 3 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

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

What is the most Operating System (OS) which can be INSTALL on Tiny hard devices like Raspberry Pi (RPi) hardware ?

I'm targeting to deploy a mesh network and manually configure MANET routing protocols. I'm preparing scenarios, architectures, and hard devices needed to do that. Are there some step-by-step...

03 March 2021 1,931 5 View

Can we classify HV and LV lines based on line length?

I have dataset which shows the length of power lines. I need to classify the lines based on the line length. Is there a rule to classify the High voltage (HV) and low voltage (LV) lines based on...

03 March 2021 4,116 4 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

Resistor definition in Piezoelectric bimorph with ANSYS workbench

Hello, good day! I am trying to simulate similar bimorph piezoelectric harvester with below commands. However, the output power doesn't change with resistor value. Please help to find the reason. ET,10,CIRCU94,0 !SET UP RESISTOR R,1,100000 !RESISTANCE VALUE TYPE,10 !SET ELEMENT TYPE E,1,2 !CREATE RESISTOR BETWEEN NODES 1 AND 2 Thanks in advance Regards,

02 March 2021 0 0 View