Dear Justin:<div><br></div><div><br></div><div>Thank you for your answer!!</div><div>Yes, I found there is already a bond defined for CT and CT, meanwhile I am waiting response from gmx-uses. </div><div>I deleted mine!</div>
<div><br></div><div>To confirm, I cannot avoid to ask you a question again.</div><div>So, please let me explain...</div><div>Sections [ bonds ], [pairs], [angles] and etc. in the "topol.top" show the information on what interaction (and how) exist among atoms in those sections.</div>
<div>Real potential values are interpreted (assigned) when I run "grompp" to get "tpr" file.</div><div>--- Is this right?</div><div><br></div><div>If this is right, I do not understand why I am not able to have new "topol_new.top" file when I use "-pp topol_new.top" with "grompp".</div>
<div>There is no error message...</div><div>--- What does the "-pp" option generate when doing grompp-?</div><div><br></div><div>Regarding the assignment of opls_xxx to atom type is, I think, well described in the file, "csoplsaanb.itp".</div>
<div><br></div><div>Thank you again!</div><div><br></div><div><br></div><div>Sincerely</div><div><br></div><div>C Kim</div><div><br><div class="gmail_quote">On Wed, Mar 4, 2009 at 9:47 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
Tree wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear All:<br>
<br>
<br>
*[1 - Situation]*<br>
I am trying to define "stretch" between two bonded atoms (for example, in my system PE (polyethylene), C-C).<br>
<br>
*[2 - ffoplsaa.rtp file]*<br>
In ffoplsaa.rtp file, I assigned C1 > opls_136<br>
C2 > opls_135<br>
This can be done by my own idea, so it does not bother anything.<br>
And totally okay.<br>
<br>
*[3 - opls_xxx and atom type]*<br>
I found that the oplsaa interpret those "opls_xxx" atoms to atom types (which are in ffoplsaabon.itp file) as follows,<br>
opls_136 > CT<br>
opls_135 > CT.<br>
<br>
( from a file containing opls_136 CT 6 12.01100 -0.120 A 3.50000e-01 2.76144e-01<br>
opls_137 CT 6 12.01100 -0.060 A 3.50000e-01 2.76144e-01<br>
)<br>
<br>
*[4 - ffoplsaabon.itp]*<br>
Based on the information in the section [2] and [3] above, I added following two sentences in the ffoplsaabon.itp file.<br>
<br>
[ bondtypes ]<br>
; i j func b0 kb<br>
CT CT 1 0.14900 334720.0 ;<br>
<br>
</blockquote>
<br></div>
There is already a CT-CT bond defined in ffoplsaabon.itp:<br>
<br>
CT CT 1 0.15290 224262.4 ; CHARMM 22 parameter file<br>
<br>
If you don't want those parameters, make sure you comment out that line so you know which parameters you are actually using!<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
*[5 - pdb2gmx result]*<div class="im"><br>
Until the section [4], I have new ffoplsaabon.itp file, so I ran pdb2gmx for my PE system.<br>
After that, when I looked at the topology file (e.g. topol.top), I could not find any information in the [ bonds ] section (after the [ atoms ] section).<br>
In other words, topol.top shows nothing in [ bonds ] section.<br>
[ bonds ]<br>
; ai aj funct c0 c1 c2 c3<br>
1 2 1<br>
<br>
</div></blockquote>
<br>
It's not showing nothing. Atoms 1 and 2 are bonded together. As long as there are parameters defined in ffoplsaabon.itp, then grompp will interpret the topology correctly. If grompp fails, then you have identified a problem.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
*[6 - Question!]*<div class="im"><br>
I think my mistake came from section [3] or [4].<br>
(1) Would you please let me know what I did wrong...?<br>
</div></blockquote>
<br>
Nothing so far that I can see (aside from potentially duplicating parameters).<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
(2) If someone is familiar with defining stretch, angle, dihedral and torsion in ffoplsaabon.itp, would you please give me an idea on how-to?<br>
</blockquote>
<br></div>
How do you define "stretch"? The force constant for how much the bond length can deviate? Otherwise, all bonded parameters are assigned by pdb2gmx as long as all atom types are defined.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
(3) Would you please summarize how the gromacs maps opls_xxx with atom type (C, CT... etc)?<br>
<br>
</blockquote>
<br></div>
Read ffoplsaa.atp.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
*[7 - Thank you!]*<div class="im"><br>
Thank you so much your participation and help!!!<br>
<br>
<br>
Sincerely,<br>
<br>
Kim<br>
<br>
<br></div>
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</blockquote><div class="im">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</blockquote></div><br></div>