From the Carlson et al. paper where these ATP parameters were published and
through choosing the appropriate amber_X atom types from the .atp (and the
corresponding values for these types in the nb and bon .itp files). As I
mentioned previously you need to add a new O3 atom type to these files
based on the information in the Carlson paper.
If you have a look at one of the entries from the ffamberXX.rtp file and
work out how this is used by pdb2gmx it should become clear what you need
to do to add the ATP to the forcefield.
Cheers
Tom
--On Saturday, February 06, 2010 00:05:10 +0530 Chandan Choudhury
<iitd...@gmail.com> wrote:
Hi Thomas !
Creating a new entry in the .rtp, nb.itp needs charge, radius, epsilon
values etc. values. Where to get these values
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Fri, Feb 5, 2010 at 6:54 PM, Thomas Piggot <t.pig...@bristol.ac.uk>
wrote:
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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----------------------
TJ Piggot
t.pig...@bristol.ac.uk
University of Bristol, UK.
--
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