[gmx-users] ATP for

Chandan Choudhury iitdckc at gmail.com
Fri Feb 5 19:35:10 CET 2010

Hi Thomas !

Creating a new entry in the .rtp, nb.itp needs charge, radius, epsilon
values etc. values. Where to get these values


Chandan kumar Choudhury
NCL, Pune

On Fri, Feb 5, 2010 at 6:54 PM, Thomas Piggot <t.piggot at 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
> --
> Thomas Piggot
> University of Bristol, UK.
> --
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