Dear Justin:<div><br></div><div><br><br><div class="gmail_quote">On Wed, Mar 4, 2009 at 10:04 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 Justin:<br>
<br>
<br>
Thank you for your answer!!<br>
Yes, I found there is already a bond defined for CT and CT, meanwhile I am waiting response from gmx-uses. I deleted mine!<br>
<br>
To confirm, I cannot avoid to ask you a question again.<br>
So, please let me explain...<br>
Sections [ bonds ], [pairs], [angles] and etc. in the "topol.top" show the information on what interaction (and how) exist among atoms in those sections.<br>
Real potential values are interpreted (assigned) when I run "grompp" to get "tpr" file.<br>
--- Is this right?<br>
</blockquote>
<br></div>
Yes.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
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".<br>
There is no error message...<br>
</blockquote>
<br></div>
It isn't produced?</blockquote><div><br></div><div>It is produced.</div><div>However, it seems having ALL the informations from '.atp', 'bon.itp' and 'nb.itp'...</div><div>Since I guessed that I would get a "processed" topology file having information, which was blank in the original topology file, this looks pretty weird... </div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
--- What does the "-pp" option generate when doing grompp-?<br>
<br>
</blockquote>
<br></div>
The -pp option gives you a "processed" topology, explicitly showing every parameter that grompp assembled.</blockquote><div><br></div><div>Yes... That is what I understood...</div><div>Since I do not think I had an appropriate "processed" topology, I guessed that there may be different meaning.</div>
<div>Thank you for your confirmation.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Regarding the assignment of opls_xxx to atom type is, I think, well described in the file, "csoplsaanb.itp".<br>
<br>
</blockquote>
<br></div>
Is that some sort of modified form of ffoplsaanb.itp? Often times a more detailed explanation is found in the .atp file for the corresponding force field.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Thank you again!<br>
<br>
<br>
Sincerely<br>
<br>
C Kim<br>
<br></div><div><div></div><div class="h5">
On Wed, Mar 4, 2009 at 9:47 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Tree wrote:<br>
<br>
Dear All:<br>
<br>
<br>
*[1 - Situation]*<br>
I am trying to define "stretch" between two bonded atoms (for<br>
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<br>
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<br>
2.76144e-01<br>
)<br>
<br>
*[4 - ffoplsaabon.itp]*<br>
Based on the information in the section [2] and [3] above, I<br>
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>
<br>
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<br>
line so you know which parameters you are actually using!<br>
<br>
*[5 - pdb2gmx result]*<br>
<br>
Until the section [4], I have new ffoplsaabon.itp file, so I ran<br>
pdb2gmx for my PE system.<br>
After that, when I looked at the topology file (e.g. topol.top),<br>
I could not find any information in the [ bonds ] section (after<br>
the [ atoms ] section).<br>
In other words, topol.top shows nothing in [ bonds ] section.<br>
[ bonds ]<br>
; ai aj funct c0 c1 c2<br>
c3<br>
1 2 1<br>
<br>
<br>
It's not showing nothing. Atoms 1 and 2 are bonded together. As<br>
long as there are parameters defined in ffoplsaabon.itp, then grompp<br>
will interpret the topology correctly. If grompp fails, then you<br>
have identified a problem.<br>
<br>
*[6 - Question!]*<br>
<br>
I think my mistake came from section [3] or [4].<br>
(1) Would you please let me know what I did wrong...?<br>
<br>
<br>
Nothing so far that I can see (aside from potentially duplicating<br>
parameters).<br>
<br>
<br>
(2) If someone is familiar with defining stretch, angle,<br>
dihedral and torsion in ffoplsaabon.itp, would you please give<br>
me an idea on how-to?<br>
<br>
<br>
How do you define "stretch"? The force constant for how much the<br>
bond length can deviate? Otherwise, all bonded parameters are<br>
assigned by pdb2gmx as long as all atom types are defined.<br>
<br>
<br>
(3) Would you please summarize how the gromacs maps opls_xxx<br>
with atom type (C, CT... etc)?<br>
<br>
<br>
Read ffoplsaa.atp.<br>
<br>
-Justin<br>
<br>
*[7 - Thank you!]*<br>
<br>
Thank you so much your participation and help!!!<br>
<br>
<br>
Sincerely,<br>
<br>
Kim<br>
<br>
<br>
------------------------------------------------------------------------<br>
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-- ========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
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</div></blockquote><div><div></div><div class="h5">
<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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