Dear Justin and gmx-users:<div><br></div><div><br></div><div>Thank you for your answer, Justin.</div><div><br></div><div>Since I corrected error related to "blank" in the input files (pdb and etc.), it has never given me "segmentation fault."</div>
<div>So... this problem is not related to this one anyway.</div><div><br></div><div>Now, I will try to correct others by following your suggestion.</div><div><br></div><div>After trying, I will contact you again... :)</div>
<div><br></div><div>Thank you again!!</div><div><br></div><div><br></div><div>Sincerely yours,</div><div><br></div><div>C Kim</div><div><br><div class="gmail_quote">On Tue, Mar 3, 2009 at 9:09 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>
Chansoo Kim 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 reply.<br>
I was too urgent, so I did not clarify my questions.<br>
Sorry about that.<br>
<br>
I totally understand how topology files (tdb, hdb, and etc..) work, but I do not clearly understand chemical reaction, which I have to define in those files...<br>
<br>
</blockquote>
<br></div>
No chemical reactions occur :) See comments embedded below<div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
[Situation]<br>
I want to do simulate polyethylene (PE) using Gromacs and OPLS-AA force field...<br>
<br>
[Topology files and etc]<br>
(1) rtp file<br>
<br>
[ Eth ]<br>
[ atoms ]<br>
C1 opls_136 -0.120 1<br>
H11 opls_140 0.060 1<br>
H12 opls_140 0.060 1<br>
C2 opls_136 -0.120 2<br>
H21 opls_140 0.060 2<br>
H22 opls_140 0.060 2<br>
[ bonds ]<br>
C1 H11<br>
C1 H12<br>
C1 C2<br>
C2 H21<br>
C2 H22<br>
C2 +C1<br>
<br>
<br>
(2) hdb file<br>
Eth 2<br>
2 6 H1 C1 C2 +C1<br>
2 6 H2 C2 C1 -C2<br>
<br>
<br>
(3) -c.tdb file<br>
<br>
[ Eth ]<br>
[ replace ]<br>
C1 opls_135 12.011 -0.18<br>
[ add ]<br>
3 4 H1 C1 C2<br>
opls_140 1.008 0.06<br>
[ delete ]<br>
H21<br>
H22<br>
<br>
<br>
(4) -n.tdb file<br>
<br>
[ Eth ]<br>
[ replace ]<br>
C2 opls_135 12.011 -0.18<br>
[ add ]<br>
3 4 H2 C2 C1<br>
opls_140 1.008 0.06<br>
[ delete ]<br>
H21<br>
H22<br>
<br>
</blockquote>
<br></div></div>
Note that the message you referenced in your first post (which provided you with this .rtp entry) resulted in a segmentation fault, therefore indicating that it probably won't work.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
(5) input pdb file<br>
<br>
ATOM 1 C1 Eth 1 1.000 1.540 0.000<br>
<br>
ATOM 2 C2 Eth 1 2.456 2.041 0.000<br>
ATOM 3 C1 Eth 2 2.456 3.581 0.000<br>
ATOM 4 C2 Eth 2 3.912 4.083 0.000<br>
ATOM 5 C1 Eth 3 3.912 5.623 0.000<br>
ATOM 6 C2 Eth 3 5.368 6.124 0.000<br>
END<br>
<br>
<br>
[Error]<br>
When I did run the pdb2gmx, I got the following error.<br>
"Atom -C not found in residue PEth1 while adding hydrogens"<br>
<br>
[Question #1 and #2]<br>
Therefore, what I should define more...?<br>
What does the "+" and "-" mean here?<br>
</blockquote>
<br></div>
+ means next residue, - means previous.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
[If...]<br>
If I change the hdb file as follows,<br>
<br>
Eth 2<br>
2 6 H1 C1 C2 C1<br>
2 6 H2 C2 C1 C2<br>
<br>
<br>
After doing pdb2gmx, I got only 12 H-atoms (which means my terminal did NOT work...).<br>
And those positions are all (0, 0, 0).<br>
<br>
</blockquote>
<br></div>
Right, because H positioning in a polymer chain may depend on previous (-) or subsequent (+) residues, so the code doesn't know where to put them.<div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Following is the results,<br>
<br>
LE Giving Russians Opium May Alter Current Situation<br>
MODEL 1<br>
ATOM 1 C1 PEt 1 1.000 0.000 0.000 1.00 0.00<br>
ATOM 2 H11 PEt 1 0.000 0.000 0.000 1.00 0.00<br>
ATOM 3 H12 PEt 1 0.000 0.000 0.000 1.00 0.00<br>
ATOM 4 C2 PEt 1 2.450 6.000 1.000 1.00 0.00<br>
ATOM 5 H21 PEt 1 0.000 0.000 0.000 1.00 0.00<br>
ATOM 6 H22 PEt 1 0.000 0.000 0.000 1.00 0.00<br>
ATOM 7 C1 PEt 2 2.450 6.000 1.000 1.00 0.00<br>
ATOM 8 H11 PEt 2 0.000 0.000 0.000 1.00 0.00<br>
ATOM 9 H12 PEt 2 0.000 0.000 0.000 1.00 0.00<br>
ATOM 10 C2 PEt 2 3.910 2.000 3.000 1.00 0.00<br>
ATOM 11 H21 PEt 2 0.000 0.000 0.000 1.00 0.00<br>
ATOM 12 H22 PEt 2 0.000 0.000 0.000 1.00 0.00<br>
ATOM 13 C1 PEt 3 3.910 2.000 3.000 1.00 0.00<br>
ATOM 14 H11 PEt 3 0.000 0.000 0.000 1.00 0.00<br>
ATOM 15 H12 PEt 3 0.000 0.000 0.000 1.00 0.00<br>
ATOM 16 C2 PEt 3 5.360 8.000 4.000 1.00 0.00<br>
ATOM 17 H21 PEt 3 0.000 0.000 0.000 1.00 0.00<br>
ATOM 18 H22 PEt 3 0.000 0.000 0.000 1.00 0.00<br>
TER<br>
ENDMDL<br>
<br>
[Question #3 from If... section ]<br>
I guess that I have to change hdb and tdb files.<br>
Would you please give some guide on that...?<br>
<br>
</blockquote>
<br></div></div>
Knowing that many people have tried to define PE with .tdb entries (and I think success is limited), I would suggest the following. Define distinct .rtp entries for the caps of your chain. Don't bother with -n.tdb and -c.tdb; I don't know how well the Gromacs code handles non-protein termini (maybe it works, but it seems to give fits for polymers). The .rtp entry for PE you've shown above seems reasonable enough for a PE monomer within the chain, but may require some tweaking (since I've never tried, I don't know).<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 for your care!<br>
<br>
<br>
Sincerely yours,<br>
<br>
C Kim<br>
<br></div><div><div></div><div class="h5">
On Tue, Mar 3, 2009 at 8:35 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>
Chansoo Kim wrote:<br>
<br>
Dear Dr. Benkova and others:<br>
<br>
<br>
I am C. Kim and trying to simulation polymer system.<br>
<br>
Since I guessed that polyethylene (PE) is a simple system, it<br>
could be not that hard to simulate it in Gromacs.<br>
Trying to do, I have read Dr. Benkova's articles in gmx-users<br>
mailing list to tackle my problems.<br>
Sorry to say, I could not solve problems, so I am asking your help!<br>
<br>
Actually I have used your files written in followings,<br>
<br>
<a href="http://www.mail-archive.com/gmx-users@gromacs.org/msg12204.html" target="_blank">http://www.mail-archive.com/gmx-users@gromacs.org/msg12204.html</a><br>
<br>
[Q1]<br>
After getting the result from the pdb2gmx, I could not see any<br>
H-atoms in my system.<br>
All the H-atoms have 0, 0, 0 positions!<br>
Therefore, my question is<br>
how I should define hdb?<br>
<br>
<br>
The .hdb file format is explained in the manual.<br>
<br>
<br>
<br>
[Q2]<br>
When I use -C2, and +C1 in hdb file, I always meet error.<br>
<br>
<br>
What is the error?<br>
<br>
-Justin<br>
<br>
Is there any other things to add to the ffopls*.* files...?<br>
<br>
Thank you for your care!<br>
<br>
<br>
Sincerely<br>
C. Kim<br>
<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>
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