[gmx-users] ATP for

Thomas Piggot t.piggot at bristol.ac.uk
Mon Feb 8 16:04:57 CET 2010


Are you sure you added it up correctly? I get a number very close to -4.

There is no hydrogen on the gamma phosphate as it was parameterised in 
this way. If the environment in which your ATP is located suggests that 
the gamma phosphate should be protonated then you need to use other ATP 
parameters which include this hydrogen (such as those in the GROMOS 
forcefield).

Cheers

Tom

Chandan Choudhury wrote:
> 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.prep 
> file 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 
> <mailto: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 <mailto: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 <mailto:t.piggot at bristol.ac.uk>>
>         wrote:
> 
>         Not sure about amb2gmx.pl <http://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> <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.
>         --
>         gmx-users mailing list    gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>         http://lists.gromacs.org/mailman/listinfo/gmx-users
>         Please search the archive at http://www.gromacs.org/search
>         before posting!
>         Please don't post (un)subscribe requests to the list. Use the www
>         interface or send it to gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>.
>         Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
> 
> 
>     ----------------------
>     TJ Piggot
> 
>     t.piggot at bristol.ac.uk <mailto:t.piggot at bristol.ac.uk>
>     University of Bristol, UK.
> 
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/search before
>     posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 

-- 
Thomas Piggot
University of Bristol, UK.



More information about the gromacs.org_gmx-users mailing list