How to design hairpin model structure for DNA

I want to simulate hairpin DNA with drug complex, but I found it difficult to design pdb file for hairpin DNA. I tried few available online resources but can not design, the sequence I am using is...

07 August 2017 2,324 7 View

Interaction energy from md trajectories.

I used namdenergy plugin in vmd to extract total, vdw and electrostatic energy. I am confused to know about the energy provided by apbs/mmpbsa. How it is different from the data obtained from...

09 October 2016 3,405 3 View

How can I build model for coarse grain simulation for graphene?

I want to build graphene coarse grain system. I tried CG builder, but for CG builder I need initial pdb, that I tried to build using VMD nanotube builder, I can build the model, however when i...

04 May 2016 2,001 5 View

How to make double stranded cDNA from single stranded cDNA?

03 April 2016 5,477 8 View

What kind of raman shift could be observed from peptide?

I had a peptide, I am trying to get raman spectra of peptide, I found in literature, the shift in peak could be observed. What kind of shift could be observed red/blue and Why? I had done some...

09 October 2015 4,447 5 View

How do I calculate the number of close contact and contact area between receptor and ligand?

02 March 2015 2,836 7 View

Can we do umbrella sampling and SMD by CHARMM or NAMD?

I want to do Umbrella Sampling (US) using NAMD, my confusion is as follows: 1. US can be perform using SMD, therefore, how to decide the SMD config file input is correct or not? What input CV or...

10 November 2014 5,450 3 View

Can anyone help me to design a new force field for a small organic/inorganic molecule for NAMD?

06 July 2014 8,981 16 View

If we want to know the result output from a NAMD simulation, what different results could be obtained?

I am new to NAMD and recently run a simulation of DNA-organic molecule interactions in NAMD for 20 ns. I want to know what the different results are that I should analyze using the output of the...

05 June 2014 1,975 6 View

How are the parameter files for new force field constructed?

I need to know the procedure and required tools for the construction .par, .inp, .tcl files

10 November 2013 6,960 2 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 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

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

Does anyone know HRM channel in a 2 plex QIAGEN Rotor- Gene Q qPCR can be used as a separate channel?

I am going to have 3 different probes in my qPCR work that I am going to do. But I realized that the machine we have in the lab is a Rotor-Gene Q 2plex HRM Platform, saying it has green, yellow,...

01 March 2021 8,544 1 View

In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein?

Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...

01 March 2021 8,747 4 View