How to make double stranded DNA from a single strand?

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Among NVT and NPT ensemble which one is preferable during MD simulation?

NVT and NPT are two commonly used ensemble during MD simulation of biomolecules. NPT must be used during equilibration just before changing to constant volume ensemble. So during production run...

06 July 2014 8,181 30 View

DNA minor grooove calculation by Curve+

I am analyzing DNA minor groove width using Curve+. Can anyone please help me to know how it calculate DNA minor groove width.

31 December 2012 9,631 7 View

How to insert a mutation into a protein dimer?

I have a dimer protein and I have to insert three amino acid residues in both monomers of the dimer at the same position. So, can anybody please suggest how to conduct this procedure without...

11 December 2012 7,817 7 View

Water asisted enzymatic substrate reduction-dehydration?

Hi, I am studying a enzymatic substrate reduction-dehydration reaction using DFT. Small model is generated from clustering of MD simulation trajectory. In small model there is a water (water-1)...

01 January 1970 583 6 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

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

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

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10?

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10? Since, the growth curve from day 2 to 10 won't be like the "Logistic curve" it might not follow logistic...

03 March 2021 1,401 3 View

After a reference from Int J Body Compos Res, can any body help?

Hi, I am after the reference below, my library says it cannot obtain a copy either locally or internationally, any help appreciated! Chris Wang ZM, Heshka S, Wielopolski L, Pi-Sunyer FX, Pierson...

03 March 2021 6,193 1 View

What techniques can I use to determine the miscibility of polymer blends?

The term miscibility refers to the single-phase state in thermodynamics. I do not mean the compatibility of different components. To determine the miscibility I know several techniques such as...

03 March 2021 4,107 4 View

Oriol Fornés

You can do a couple of things here:

1) You can download the biological unit of the PDB from ftp://ftp.wwpdb.org/pub/pdb/data/biounit/coordinates/all/.

2) You can calculate the coordinates of the missing subunits from the BIOMT transformation matrices contained in the pdb file.

If you are planning on doing the 2nd option, I highly recommend the usage of the following server: http://watcut.uwaterloo.ca/cgi-bin/makemultimer/. I guess the script MakeMultimer.py can also be downloaded from the internet.