I was also interested in this, and had posted a message about this. I am interested, like the OP, in an isolated nucleotide molecule, such as cytosine or guanidine. Does one have to construct a completely new topology for this? <div>
<br><br><div class="gmail_quote">On Fri, Mar 18, 2011 at 9:04 PM, <span dir="ltr"><<a href="mailto:nishap.patel@utoronto.ca">nishap.patel@utoronto.ca</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
I know and I apologize, I mistyped. It is an isolated molecule. I did try to combine the parameters of OPLSAA of carbohydrates(Jorgensen, 1997) with the nucleotide base paper (Jorgensen, 1991). However, I am not sure the partial charge that I should use on the Carbon (C) atom of the sugar molecule that is linked with the Nitrogen (N) of nucleoside, because it is not an alcohol anymore.<div>
<div></div><div class="h5"><br>
<br>
<br>
<br>
<br>
Quoting David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>>:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
On 2011-03-18 20.41, <a href="mailto:nishap.patel@utoronto.ca" target="_blank">nishap.patel@utoronto.ca</a> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I apologize, but I am trying to simulate Cytidine (not cytosine). The<br>
parameters are given for cytosine.<br>
<br>
</blockquote>
That's not what you asked for, but in that case you have to combine the<br>
cytosine parameters with some kind of sugar ring. Is this in a polymer<br>
through the sugar rings as well, or an isolated molecule?<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Nisha<br>
<br>
<br>
<br>
Quoting David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>>:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
On 2011-03-18 20.14, <a href="mailto:nishap.patel@utoronto.ca" target="_blank">nishap.patel@utoronto.ca</a> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello,<br>
<br>
I am trying to use OPLS-AA force field for simulating nucleosides eg.<br>
cytosine, adenosine etc. I found parameters for nucleotide bases (eg.<br>
1-methylcytosine) but I haven't been able to find parameters for<br>
nucleosides. Does anyone know where I can find parameters for<br>
nucleotides for OPLS-AA (if they do exist?). A paper citation would be<br>
helpful.<br>
<br>
Thanks.<br>
<br>
Nisha Patel<br>
<br>
</blockquote>
It's all there in the atomtypes.atp file, a little fragment:<br>
<br>
opls_336 12.01100 ; Cytosine C4 Nucleotide base<br>
opls_337 12.01100 ; Cytosine C5 parameters:<br>
opls_338 12.01100 ; Cytosine C6 JACS,113,2810(1991)<br>
opls_339 1.00800 ; Cytosine H-N1<br>
<br>
<br>
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