Hi Tom!!<div>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">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? </div>
<div><br></div><div>Chandan</div><div><br>--<br>Chandan kumar Choudhury<br>NCL, Pune<br>INDIA<br>
<br><br><div class="gmail_quote">On Sat, Feb 6, 2010 at 1:13 AM, TJ 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;">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
>From the Carlson et al. paper where these ATP parameters were published and <br>
</blockquote>
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.<br>
<br>
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.<br>
<br>
Cheers<br>
<br>
Tom<div><div></div><div class="h5"><br>
<br>
--On Saturday, February 06, 2010 00:05:10 +0530 Chandan Choudhury <<a href="mailto:iitdckc@gmail.com" target="_blank">iitdckc@gmail.com</a>> wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Hi Thomas !<br>
<br>
Creating a new entry in the .rtp, nb.itp needs charge, radius, 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 <<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> or acpypi but you 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 entry in<br>
the .rtp and then also add the appropriate bonded parameters into the<br>
bon.itp file, making sure to include the bonded parameters for the new O3<br>
atom type. Do note that you need to also add this new atom type for the<br>
O3 oxygen into the .atp file and the non-bonded parameters for 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 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 atp.prep and<br>
frcmod.phos for ATP can be found at<br>
<a href="http://www.pharmacy.manchester.ac.uk/bryce/amber" target="_blank">http://www.pharmacy.manchester.ac.uk/bryce/a</a></blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<font class="Apple-style-span" color="#551A8B"><u>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</u></font></blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<a href="http://www.pharmacy.manchester.ac.uk/bryce/amber" target="_blank">mber</a>. How can I use it in<br>
ffamber.<br>
The program <a href="http://amb2gmx.pl" target="_blank">amb2gmx.pl</a> <<a href="http://amb2gmx.pl" target="_blank">http://amb2gmx.pl</a>> 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></div></div>
----------------------<br>
TJ Piggot<div class="im"><br>
<a href="mailto:t.piggot@bristol.ac.uk" target="_blank">t.piggot@bristol.ac.uk</a><br></div><div><div></div><div class="h5">
University of Bristol, UK.<br>
<br>
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