Thanks Tom.<div>Some how only the negative charges were being added in spreadsheet. So, I got charge around -12. </div><div>I am simulating 1QHH. It has ATP in it, the structure of the ligand in the rcsb (<a href="http://www.pdb.org/pdb/explore/explore.do?structureId=1QHH">http://www.pdb.org/pdb/explore/explore.do?structureId=1QHH</a>) shows ATP with hydrogen.</div>
<div><br></div><div> <br clear="all"><br>--<br>Chandan kumar Choudhury<br>NCL, Pune<br>INDIA<br>
<br><br><div class="gmail_quote">On Mon, Feb 8, 2010 at 8:34 PM, Thomas Piggot <span dir="ltr"><<a href="mailto:t.piggot@bristol.ac.uk">t.piggot@bristol.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Are you sure you added it up correctly? I get a number very close to -4.<br>
<br>
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).<div class="im">
<br>
<br>
Cheers<br>
<br>
Tom<br>
<br>
Chandan Choudhury wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Hi Tom!!<br>
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 <a href="http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/ATP.prep" target="_blank">http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/ATP.prep</a> file is -12.7145. How come fractional? and the hydrogens of phosphate are missing. How can it be overcome? <br>
Chandan<br>
<br>
--<br>
Chandan kumar Choudhury<br>
NCL, Pune<br>
INDIA<br>
<br>
<br></div><div class="im">
On Sat, Feb 6, 2010 at 1:13 AM, TJ Piggot <<a href="mailto:t.piggot@bristol.ac.uk" target="_blank">t.piggot@bristol.ac.uk</a> <mailto:<a href="mailto:t.piggot@bristol.ac.uk" target="_blank">t.piggot@bristol.ac.uk</a>>> wrote:<br>
<br>
>From the Carlson et al. paper where these ATP parameters were<br>
published and<br>
<br>
through choosing the appropriate amber_X atom types from the .atp<br>
(and the corresponding values for these types in the nb and bon .itp<br>
files). As I mentioned previously you need to add a new O3 atom type<br>
to these files based on the information in the Carlson paper.<br>
<br>
If you have a look at one of the entries from the ffamberXX.rtp file<br>
and work out how this is used by pdb2gmx it should become clear what<br>
you need to do to add the ATP to the forcefield.<br>
<br>
Cheers<br>
<br>
Tom<br>
<br>
<br>
--On Saturday, February 06, 2010 00:05:10 +0530 Chandan Choudhury<br></div><div class="im">
<<a href="mailto:iitdckc@gmail.com" target="_blank">iitdckc@gmail.com</a> <mailto:<a href="mailto:iitdckc@gmail.com" target="_blank">iitdckc@gmail.com</a>>> wrote:<br>
<br>
<br>
Hi Thomas !<br>
<br>
Creating a new entry in the .rtp, nb.itp needs charge, radius,<br>
epsilon<br>
values etc. values. Where to get these values<br>
<br>
<br>
Chandan<br>
<br>
--<br>
Chandan kumar Choudhury<br>
NCL, Pune<br>
INDIA<br>
<br>
<br>
<br>
On Fri, Feb 5, 2010 at 6:54 PM, Thomas Piggot<br></div>
<<a href="mailto:t.piggot@bristol.ac.uk" target="_blank">t.piggot@bristol.ac.uk</a> <mailto:<a href="mailto:t.piggot@bristol.ac.uk" target="_blank">t.piggot@bristol.ac.uk</a>>><br>
wrote:<br>
<br>
Not sure about <a href="http://amb2gmx.pl" target="_blank">amb2gmx.pl</a> <<a href="http://amb2gmx.pl" target="_blank">http://amb2gmx.pl</a>> or acpypi but you<div><div></div><div class="h5"><br>
can do this by hand. Consult<br>
the GROMACS manual (Chapter 4) for the equations to convert the<br>
parameters into GROMACS format.<br>
<br>
I would also say that the easiest way would be to create a new<br>
entry in<br>
the .rtp and then also add the appropriate bonded parameters<br>
into the<br>
bon.itp file, making sure to include the bonded parameters for<br>
the new O3<br>
atom type. Do note that you need to also add this new atom type<br>
for the<br>
O3 oxygen into the .atp file and the non-bonded parameters for<br>
the atom<br>
type into the nb.itp file.<br>
<br>
You can also add entries into the .hdb to allow pdb2gmx to add the<br>
appropriate hydrogens to your ATP if so desired. If not, your<br>
input pdb<br>
for pdb2gmx will need to have these hydrogens already included.<br>
<br>
Cheers<br>
<br>
Tom<br>
<br>
Chandan Choudhury wrote:<br>
<br>
<br>
Hello gmx users,<br>
I need to use ATP's parameter for amber port in gromacs. The<br>
atp.prep and<br>
frcmod.phos for ATP can be found at<br>
<a href="http://www.pharmacy.manchester.ac.uk/bryce/a" target="_blank">http://www.pharmacy.manchester.ac.uk/bryce/a</a><br></div></div>
<<a href="http://www.pharmacy.manchester.ac.uk/bryce/amber" target="_blank">http://www.pharmacy.manchester.ac.uk/bryce/amber</a>><br>
<br>
_mdrun -s spc_25_eq.tpr -cpi state.cpi -c spc_25_eq.pdb -o<div class="im"><br>
spc_25_eq.trr -e spc_25_eq.edr -g spc_25_eq.log -append yes_<br>
<br></div>
mber <<a href="http://www.pharmacy.manchester.ac.uk/bryce/amber" target="_blank">http://www.pharmacy.manchester.ac.uk/bryce/amber</a>>. How can<div class="im"><br>
I use it in<br>
ffamber.<br></div>
The program <a href="http://amb2gmx.pl" target="_blank">amb2gmx.pl</a> <<a href="http://amb2gmx.pl" target="_blank">http://amb2gmx.pl</a>> <<a href="http://amb2gmx.pl" target="_blank">http://amb2gmx.pl</a>><div class="im">
<br>
needs amber to be installed,<br>
which is not present. Same with ACPYPI.<br>
<br>
<br>
Any suggestion will be very helpful.<br>
<br>
Chandan<br>
<br>
<br>
--<br>
Chandan kumar Choudhury<br>
NCL, Pune<br>
INDIA<br>
<br>
<br>
<br>
--<br>
Thomas Piggot<br>
University of Bristol, UK.<br>
--<br>
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<br>
<br>
<br>
<br>
<br>
----------------------<br>
TJ Piggot<br>
<br></div>
<a href="mailto:t.piggot@bristol.ac.uk" target="_blank">t.piggot@bristol.ac.uk</a> <mailto:<a href="mailto:t.piggot@bristol.ac.uk" target="_blank">t.piggot@bristol.ac.uk</a>><div class="im"><br>
University of Bristol, UK.<br>
<br>
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<br>
<br>
</div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
Thomas Piggot<br>
University of Bristol, UK.<br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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</div></div></blockquote></div><br></div>