I can't say much about ATP and ADP specifically, but one general piece
of advice I have about topology files for small molecules is that
prodrg doesn't
necessarily place all of the hydrogens if they're not initially
present, which inevitably results in problems in some cases. There are
a variety of programs which can protonate molecules, so you might try
one of those. I've also had some success in some cases using OpenEye's
"convert" (<a href="http://demo.eyesopen.com/cgi-bin/convert/convert.out">http://demo.eyesopen.com/cgi-bin/convert/convert.out</a>), but
it doesn't generate GROMACS topology files. Perhaps someone will have
more general suggestions.<br>
<br>
About charges, my sense is that it's probably not wise to use charges
from prodrg. I would probably try to use some package which computes
more sensible quantum mechanical charges which are more similar to
those used in parameterizing force fields. See this note from the FAQ
for prodrg:<br>
<br>
<font size="3"> Q: The atomic charges don't always come out right?<p>
A: This is a well known limitation. PRODRG works with the concept of charge
groups, which are defined as a group of bonded atoms with an integer charge.
E.g. -COO would have the C (with a slight positive charge) and the two
O's (with an equal negative charge) in one "charge group" with the total
charge being -1. Thus in order for PRODRG to assign atomic charges it needs
to be able to recognise the charge groups first. This is particularly difficult
in ring systems with nitrogens, and several charge group definitions (e.g.
C-Cl) or still missing. I would definitely recommend that you check these
charges before starting your 2 microsecond simulation.<br>
</p>
<p>____</p>
</font>I haven't been using OPLS, myself; I'm actually using the AMBER
force field, but my usual method for setting up topologies is this:<br>
1) Generate a mol2 file of the small molecule, including hydrogens (sometimes using OpenEye's convert).<br>
2) Use AMBER's antechamber package to calculate AM1-BCC charges and generate amber topologies, as well as do atom typing.<br>
3) Convert AMBER topologies to GROMACS topologies using the AMBER ff. <br>
<br>
This isn't as crazy as it sounds since I'm using the AMBER ff. But
others on the list may have a better procedure for generating
topologies directly in GROMACS. I think your problem is really with
step 2-3, and there must be other packages that can do this easily.<br>
<br>
David<br>
<br>
<br><div><span class="gmail_quote">On 11/17/05, <b class="gmail_sendername">TJ Piggot</b> <<a href="mailto:t.piggot@bristol.ac.uk" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">t.piggot@bristol.ac.uk
</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi I sent this email a few weeks ago and have had no replies yet I hope<br>that someone will be able to help this time.<br><br>I am trying to construct ATP and ADP topology files for use with the opls<br>force field. I have previously been able to do this for the ffG43a1 force
<br>field using prodrg.<br><br>However prodrg does not produce output files for use with the opls force<br>field. I have tried to change the prodrg output files (.itp) for ADP and<br>ADP but the problem is that there is not enough atoms as the individual
<br>hydrogens are not defined.<br><br>Can i change this .itp to include the hydrogens and if so what values do i<br>need to use for the charges and masses of these new atoms ?<br><br>Also if anyone has already constructed these topology files and could send
<br>them to me i would be very grateful.<br><br>Thanks in advance<br><br>Tom Piggot<br><br>----------------------<br>TJ Piggot<br><a href="mailto:t.piggot@bristol.ac.uk" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
t.piggot@bristol.ac.uk</a><br>_______________________________________________
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