[gmx-users] ATP for

[Chandan Choudhury]

Hi Tom!!
Thanks for the information. I went through the paper and added the new O3
atom type.  One unusual thing I noticed was that the sum of the partial
charges on the atoms of AT P at the last column of
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/ATP.prepfile
is       -12.7145. How come fractional? and the hydrogens of phosphate
are missing. How can it be overcome?

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Sat, Feb 6, 2010 at 1:13 AM, TJ Piggot <t.piggot at bristol.ac.uk> wrote:

>  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 <
> iitdckc at 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.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/a<http://www.pharmacy.manchester.ac.uk/bryce/amber>
>
> *mdrun -s spc_25_eq.tpr -cpi state.cpi -c  spc_25_eq.pdb -o spc_25_eq.trr
>> -e spc_25_eq.edr -g spc_25_eq.log  -append yes*
>
> mber <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.piggot at bristol.ac.uk
> University of Bristol, UK.
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
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