[gmx-users] ATP for
Thomas Piggot
t.piggot at bristol.ac.uk
Mon Feb 8 17:29:24 CET 2010
Well it is up to you to decide (or find out) if you think it should be
protonated or not. I just had a quick look in the PDB file and there are
no hydrogens on the ATP, plus the crystal structure was determined using
an ATP analogue so I would not solely base my judgement on a structure
of the ATP shown on the website which may contain a hydrogen on the
gamma phosphate.
Tom
Chandan Choudhury wrote:
> Thanks Tom.
> Some how only the negative charges were being added in spreadsheet. So,
> I got charge around -12.
> I am simulating 1QHH. It has ATP in it, the structure of the ligand in
> the rcsb (http://www.pdb.org/pdb/explore/explore.do?structureId=1QHH)
> shows ATP with hydrogen.
>
>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> On Mon, Feb 8, 2010 at 8:34 PM, Thomas Piggot <t.piggot at bristol.ac.uk
> <mailto:t.piggot at bristol.ac.uk>> wrote:
>
> 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>
> <mailto: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>
> <mailto: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>
> <mailto:t.piggot at bristol.ac.uk <mailto:t.piggot at bristol.ac.uk>>>
> wrote:
>
> Not sure about amb2gmx.pl <http://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> <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 <mailto:t.piggot at bristol.ac.uk>
> <mailto:t.piggot at bristol.ac.uk <mailto:t.piggot at bristol.ac.uk>>
>
> University of Bristol, UK.
>
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>
> --
> Thomas Piggot
> University of Bristol, UK.
> --
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--
Thomas Piggot
University of Bristol, UK.
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