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.pig...@bristol.ac.uk
<mailto:t.pig...@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.pig...@bristol.ac.uk <mailto:t.pig...@bristol.ac.uk>
<mailto:t.pig...@bristol.ac.uk <mailto:t.pig...@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
<iitd...@gmail.com <mailto:iitd...@gmail.com>
<mailto:iitd...@gmail.com <mailto: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 <mailto:t.pig...@bristol.ac.uk>
<mailto:t.pig...@bristol.ac.uk <mailto:t.pig...@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.pig...@bristol.ac.uk <mailto:t.pig...@bristol.ac.uk>
<mailto:t.pig...@bristol.ac.uk <mailto:t.pig...@bristol.ac.uk>>
University of Bristol, UK.
-- gmx-users mailing list gmx-users@gromacs.org
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--
Thomas Piggot
University of Bristol, UK.
--
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--
Thomas Piggot
University of Bristol, UK.
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