Dear Rainer,<br><br>Thankyou very much. I read the abstract of this paper and it says torsional parameters fro alkanes have been updated. I do not have access to full contents of this paper, so could not get it.<br>Thanks again.<br>
<br>Sulatha<br><br><div class="gmail_quote">On Wed, Feb 9, 2011 at 2:27 PM, Rainer Boeckmann <span dir="ltr"><<a href="mailto:rainer.boeckmann@biologie.uni-erlangen.de">rainer.boeckmann@biologie.uni-erlangen.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div style="word-wrap: break-word;"><div class="im">Dear Sulatha,<br><br>these are probably the more recent parameters from<br>
<br>Price, M. L. P., D. Ostrovsky, and W. L. Jorgensen. 2001. Gas-phase and liquid-state properties of<br>8esters, nitriles, and nitro compounds with the opls-aa force field. J. Comput. Chem. 22:1340–<br>1352.<br><br>Best<br>
Rainer<br></div><div><div class="im"><div><br></div><div>On Feb 9, 2011, at 6:48 AM, sulatha M. S wrote:</div><br></div><blockquote type="cite"><div><div></div><div class="h5">I looked at the the paper published in 1999, ( Jorgensen et al JACS, 121, 20, 4831, 1999), the aliphatic torsional parameters are the same as those from 1996. here are the values,<br>
<br><br> V1 V2 V3 (kcal/mol)<br>
CT-CT-CT-CT 1.740 -0.157 0.279<br><br>HC-CT-CT-CT 0.000 0.000 0.366<br><br>HC-CT-CT-HC 0.000 0.000 0.318<br>
<br><br>Values calculated from the equation given in p.62 of the manual in kJ/mol are <br><br> c0 c1 c2 c3<br>
CT-CT-CT-CT 3.56686 -1.88907 0.65688 -2.33467<br>
<br>
HC-CT-CT-CT 0.66526 1.99577 0.000 -2.66102<br>
<br>
HC-CT-CT-HC 0.76567 -2.29702 0.000 -3.06269<br><br>and the values given in ffoplsaabon.itp are:<br><br>CT-CT-CT-CT 2.9288 -1.4644 0.2092 -1.6736<br>
<br>
HC-CT-CT-CT 0.6276 1.88280 0.000 -2.5104<br>
<br>
HC-CT-CT-HC 0.6276 1.8828 0.000 -2.5104<br><br>So there is a difference. Which of these is correct ? Any help is highly appreciated.<br><br>Sulatha<br><br><br><br><div class="gmail_quote">
On Tue, Feb 8, 2011 at 7:48 PM, Andrew Paluch <span dir="ltr"><<a href="mailto:apaluch@nd.edu" target="_blank">apaluch@nd.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
There is no error. The alkane dihedral parameters were updated in 1999, and differ from those originally published in 1996.<br><br>Andrew<br><br><div class="gmail_quote"><div><div></div><div>On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S <span dir="ltr"><<a href="mailto:mssulatha@gmail.com" target="_blank">mssulatha@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div>Hi all,<br><pre>Hi</pre><pre> </pre><pre>I've converted the OPLS-AA torsional potential parameters for the</pre>
<pre>alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation),</pre><pre>C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the</pre>
<pre>OPLS format given in Jorgensen et al, JACS 118, 11225 (1996) </pre><pre>to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found</pre><pre>that the calculated values are different.</pre><pre> </pre><pre>A previous post to the gmx-users mailing list on March 27, 2008,</pre>
<pre>pointed out this issue for the H-C-C-H torsional potential but there was no response to that.</pre><pre> </pre><pre>Does anyone know if there is an error in the ffoplsaabon.itp file? Or</pre><pre>is there a newer set of OPLS-AA parameters?</pre>
<pre> </pre><pre>For the OPLS-AA parameters (in kcal/mol), I used:</pre><pre> </pre><pre>dihedral<span> </span>V1<span> </span>V2<span> </span>V3</pre><pre>C-C-C-C<span> </span>1.740<span> </span>-0.157<span> </span>0.279</pre>
<pre>C-C-C-H<span> </span>0.0<span> </span>0.0<span> </span>0.366</pre><pre>H-C-C-H<span> </span>0.0<span> </span>0.0<span> </span>0.318</pre>
<pre> </pre><pre>from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as:</pre><pre> </pre><pre>dihedral<span> </span>C0<span> </span><span> </span>C1<span> </span>C2<span> </span>C3</pre>
<pre>C-C-C-C<span> </span>3.56686<span> </span>-1.889076<span> </span>0.65688 <span> </span>-2.33467</pre><pre>C-C-C-H<span> </span>0.66526<span> </span>1.99577<span> </span>0.0<span> </span>-2.661024</pre>
<pre>H-C-C-H<span> </span>0.76567<span> </span>-2.29702<span> </span>0.0<span> </span>-3.06269</pre><pre> </pre><pre>the parameters in the ffoplsaabon.itp file are:</pre>
<pre> </pre><pre>dihedral<span> </span>C0<span> </span>C1<span> </span>C2<span> </span>C3</pre><pre>C-C-C-C<span> </span>2.9288<span> </span>-1.4644<span> </span>0.2092<span> </span>-1.6736</pre>
<pre>C-C-C-H<span> </span>0.6276<span> </span>1.88280<span> </span>0.0<span> </span>-2.5104</pre><pre>H-C-C-H<span> </span>0.6276<span> </span>1.8828<span> </span>0.0<span> </span>-2.5104</pre>
<br><br>Thankyou for any clarification.<br><font color="#888888"><br>Sulatha<br>
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<div>__________________________________________________________<br>Prof. Dr. Rainer Böckmann<br>Computational Biology<br>Universität Erlangen-Nürnberg<br>Staudtstr. 5<br>91058 Erlangen<br></div><div>Phone: ++49 +9131 85-25409<span style="white-space: pre-wrap;"> </span> FAX: ++49 +9131 85-25410<br>
E-Mail: <a href="mailto:rainer@bioinformatik.uni-saarland.de" target="_blank">rainer.boeckmann@biologie.uni-erlangen.de</a><br><a href="http://www.biotechnik.nat.uni-erlangen.de/research/boeckmann/" target="_blank">http://www.biotechnik.nat.uni-erlangen.de/research/boeckmann/</a></div>
<div>___________________________________________________________<br><br></div></div></span></div></span></div></span></div></span></div></span></div></span></div></span></span>
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