[gmx-users] ATP for

Thomas Piggot t.piggot at bristol.ac.uk
Fri Feb 5 14:24:34 CET 2010

Not sure about amb2gmx.pl or acpypi but you can do this by hand. Consult 
the GROMACS manual (Chapter 4) for the equations to convert the 
parameters into GROMACS format.

I would also say that the easiest way would be to create a new entry in 
the .rtp and then also add the appropriate bonded parameters into the 
bon.itp file, making sure to include the bonded parameters for the new 
O3 atom type. Do note that you need to also add this new atom type for 
the O3 oxygen into the .atp file and the non-bonded parameters for the 
atom type into the nb.itp file.

You can also add entries into the .hdb to allow pdb2gmx to add the 
appropriate hydrogens to your ATP if so desired. If not, your input pdb 
for pdb2gmx will need to have these hydrogens already included.



Chandan Choudhury wrote:
> Hello gmx users,
> I need to use ATP's parameter for amber port in gromacs. The atp.prep 
> and frcmod.phos for ATP can be found at 
> http://www.pharmacy.manchester.ac.uk/bryce/amber. How can I use it in 
> ffamber.
> The program amb2gmx.pl <http://amb2gmx.pl> needs amber to be installed, 
> which is not present. Same with ACPYPI.
> Any suggestion will be very helpful.
> Chandan
> --
> Chandan kumar Choudhury
> NCL, Pune

Thomas Piggot
University of Bristol, UK.

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