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.
Cheers
Tom
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
INDIA
--
Thomas Piggot
University of Bristol, UK.
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