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Questions related from Dario Corrada
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...
07 July 2014 2,201 4 View
From what I have understood (from the AMBER manual) I have to prepare the topology of every single mutant I want to scan and, subsequently, I have to start an individual run (with the MMPBSA.py...
06 June 2014 3,614 1 View
Since I have MDs produced with GROMACS, are there available any tool for calculating dGs with MM/GBSA method? (and, in the meanwhile, without converting trajectories in AMBER format?)
02 February 2014 7,254 9 View
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...
02 February 2014 5,004 4 View
Does anyone have a "reference manual" of such forcefield? (especially the related top files in GROMACS) e.g. what are the atom types included and what they describe, etc. etc.
01 January 2014 5,613 3 View
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...
01 January 2014 2,057 9 View
I am interested in this technique. Beyond the methodological background can you suggest any reference where accelerated MD has been performed with the GROMACS package? In my lab we do not have...
12 December 2013 8,655 1 View
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...
12 December 2013 8,482 3 View
...ma 'sto paper quando uscirà???
01 January 1970 1,111 0 View
