Dario Corrada

5 Questions 38 Answers 0 Followers

Questions related from Dario Corrada

How can I convert a trajectory file from GROMACS (trr or xtc format) to AMBER (ASCII or NetCDF format)?

How can I convert a trajectory file from GROMACS (trr or xtc format) to AMBER (ASCII or NetCDF format)? I have always seen tutorial about the revers procedure, ie from AMBER to GROMACS...

11 July 2014 3,969 4 View

Can anyone help with a forcefield with halogen bonding treatments?

I am looking for a forcefield in GROMACS which better characterizes the TCDD ligand. In particular I have found that OPLS-AAx seems suitable [J Chem Theory Comput. 2012 Oct...

19 February 2014 1,744 3 View

Do you know of any similar tool to OPLS-AA for making topology file?

I need to create a topology file (.top for GROMACS) of 2,3,7,8-TCDD (dioxin). In particular my topology file will have to be suited for implementing OPLS-AA forcefield, since I know that the...

10 January 2014 3,510 8 View

Alternatives to HADDOCK for protein-protein docking?

I have to perform protein-protein docking in order to obtain a dimer from two protomer structures. Even if I can infer the interacting surfaces from homolog dimers, I have no clues about contact...

29 December 2013 382 4 View

How to graft short oligopeptidic linkers to substitute long loops?

I have to accomplish an homology modeling task in which the reference template does not cover very large loops of the query sequence (20-30 residues). I have not found any reliable alternative...

16 December 2013 8,473 2 View