On 10/11/2011 10:43 PM, James Starlight wrote:
Mark,
The problem is that my .itp done for old gromos ff consist of
parameters for molecule wich has some specific groups wich not preset
in the gromos96 ff so pdb2gmx is not good decision :)
Then you'll have to work out how the old .itp worked, and how that
functionality works in the current force field and file format. Chapters
4 and 5 are your friends here.
Mark
By the way I'm intresting what changes were done in the dihedrail
terms since gromos87 ff.
E.g I found topology wich consist of parameters for D-amino asids and
I want to compare it with L-analogs in gromos96 to find possibe way to
make such parametrisation in the gromos96
James
2011/11/10 Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
On 10/11/2011 9:30 PM, James Starlight wrote:
Dear Gromacs Users!
I need tto convert topology.itp fule made for my molecule for
the old gromos87 force field to the form wich would be
suitable for the simulation with the gromos96 force field.
What main corrections should I do in my existing .itp topology?
Use pdb2gmx with gromos96 to find out the form of the solution.
Then adapt as necessary.
Mark
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