<div>Hi Thomas !</div><div><br></div>Creating a new entry in the .rtp, nb.itp needs charge, radius, epsilon values etc. values. Where to get these values<div><br></div><div>Chandan<br clear="all"><br>--<br>Chandan kumar Choudhury<br>
NCL, Pune<br>INDIA<br>
<br><br><div class="gmail_quote">On Fri, Feb 5, 2010 at 6:54 PM, Thomas Piggot <span dir="ltr"><<a href="mailto:t.piggot@bristol.ac.uk" target="_blank">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">
Not sure about <a href="http://amb2gmx.pl" target="_blank">amb2gmx.pl</a> 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.<br>
<br>
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.<br>
<br>
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.<br>
<br>
Cheers<br>
<br>
Tom<br>
<br>
Chandan Choudhury wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>
Hello gmx users,<br>
I need to use ATP's parameter for amber port in gromacs. The atp.prep and frcmod.phos for ATP can be found at <a href="http://www.pharmacy.manchester.ac.uk/bryce/amber" target="_blank">http://www.pharmacy.manchester.ac.uk/bryce/amber</a>. How can I use it in 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>> needs amber to be installed, which is not present. Same with ACPYPI.<div>
<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>
</div></blockquote>
<br>
-- <br>
Thomas Piggot<br>
University of Bristol, UK.<br><font color="#888888">
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