Dear Justin:<div><br></div><div><br></div><div>Thank you for your reply.</div><div>I was too urgent, so I did not clarify my questions.</div><div>Sorry about that.</div><div><br></div><div>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...</div>
<div><br></div><div><br></div><div><span class="Apple-style-span" style="font-weight: bold;"><span class="Apple-style-span" style="color: rgb(255, 0, 0);">[Situation]</span></span></div><div>I want to do simulate polyethylene (PE) using Gromacs and OPLS-AA force field...</div>
<div><br></div><div><span class="Apple-style-span" style="font-weight: bold;"><span class="Apple-style-span" style="color: rgb(255, 0, 0);">[Topology files and etc]</span></span></div><div><span class="Apple-style-span" style="color: rgb(0, 0, 153);"> (1) rtp file</span></div>
<div><span class="Apple-style-span" style="font-family: -webkit-monospace; "><pre style="margin-top: 0em; margin-right: 0em; margin-bottom: 0em; margin-left: 0em; ">[ Eth ]
[ atoms ]
C1 opls_136 -0.120 1
H11 opls_140 0.060 1
H12 opls_140 0.060 1
C2 opls_136 -0.120 2
H21 opls_140 0.060 2
H22 opls_140 0.060 2
[ bonds ]
C1 H11
C1 H12
C1 C2
C2 H21
C2 H22
C2 +C1</pre><pre style="margin-top: 0em; margin-right: 0em; margin-bottom: 0em; margin-left: 0em; "><br></pre><pre style="margin-top: 0em; margin-right: 0em; margin-bottom: 0em; margin-left: 0em; "><span class="Apple-style-span" style="font-family: arial; font-size: 13px; white-space: normal; "><span class="Apple-style-span" style="color: rgb(0, 0, 153);"> (2) hdb file</span></span><span class="Apple-style-span" style="color: rgb(0, 0, 153);">
</span>Eth 2
2 6 H1 C1 C2 +C1
2 6 H2 C2 C1 -C2
</pre><div><span class="Apple-style-span" style="font-size: 12px; white-space: pre;"><br></span></div><div><span class="Apple-style-span" style="font-size: 12px; white-space: pre;"><span class="Apple-style-span" style="font-size: 13px; white-space: normal; "><pre style="margin-top: 0em; margin-right: 0em; margin-bottom: 0em; margin-left: 0em; ">
<span class="Apple-style-span" style="font-family: arial; white-space: normal; "><span class="Apple-style-span" style="color: rgb(0, 0, 153);"> (3) -c.tdb file</span></span></pre></span></span></div><div><span class="Apple-style-span" style="font-size: 12px; white-space: pre;"><span class="Apple-style-span" style="font-size: 13px; white-space: normal; "><pre style="margin-top: 0em; margin-right: 0em; margin-bottom: 0em; margin-left: 0em; ">
[ Eth ]
[ replace ]
C1 opls_135 12.011 -0.18
[ add ]
3 4 H1 C1 C2
opls_140 1.008 0.06
[ delete ]
H21
H22</pre></span></span></div><div><span class="Apple-style-span" style="font-size: 12px; white-space: pre;"><br></span></div><div><span class="Apple-style-span" style="font-size: 12px; white-space: pre;"><span class="Apple-style-span" style="font-size: 13px; white-space: normal; "><pre style="margin-top: 0em; margin-right: 0em; margin-bottom: 0em; margin-left: 0em; ">
<span class="Apple-style-span" style="font-family: arial; white-space: normal; "><span class="Apple-style-span" style="color: rgb(51, 51, 255);"> (4) -n.tdb file</span></span></pre></span></span></div></span></div><div><span class="Apple-style-span" style="font-family: -webkit-monospace; "><pre style="margin-top: 0em; margin-right: 0em; margin-bottom: 0em; margin-left: 0em; ">
[ Eth ]
[ replace ]
C2 opls_135 12.011 -0.18
[ add ]
3 4 H2 C2 C1
opls_140 1.008 0.06
[ delete ]
H21
H22</pre></span></div><div><br></div><div><span class="Apple-style-span" style="color: rgb(0, 0, 153);"> (5) input pdb file</span><span class="Apple-style-span" style="color: rgb(0, 0, 153);"><span class="Apple-style-span" style="font-family: -webkit-monospace; font-size: 12px; white-space: pre; "></span></span></div>
<div><span class="Apple-style-span" style="font-family: -webkit-monospace; font-size: 12px; white-space: pre;"><br></span></div><div><span class="Apple-style-span" style="font-family: -webkit-monospace; font-size: 12px; white-space: pre; ">ATOM 1 C1 Eth 1 1.000 1.540 0.000</span><br>
</div><div><span class="Apple-style-span" style="font-family: -webkit-monospace; "><pre style="margin-top: 0em; margin-right: 0em; margin-bottom: 0em; margin-left: 0em; ">ATOM 2 C2 Eth 1 2.456 2.041 0.000
ATOM 3 C1 Eth 2 2.456 3.581 0.000
ATOM 4 C2 Eth 2 3.912 4.083 0.000
ATOM 5 C1 Eth 3 3.912 5.623 0.000
ATOM 6 C2 Eth 3 5.368 6.124 0.000
END</pre></span></div><div><br></div><div><span class="Apple-style-span" style="color: rgb(255, 0, 0);"><span class="Apple-style-span" style="font-weight: bold;">[Error]</span></span></div><div>When I did run the pdb2gmx, I got the following error.</div>
<div>"Atom -C not found in residue PEth1 while adding hydrogens"</div><div><br></div><div><span class="Apple-style-span" style="font-weight: bold;"><span class="Apple-style-span" style="color: rgb(255, 0, 0);">[Question #1 and #2]</span></span></div>
<div>Therefore, what I should define more...?</div><div>What does the "+" and "-" mean here?</div><div><br></div><div><br></div><div><span class="Apple-style-span" style="color: rgb(255, 0, 0);"><span class="Apple-style-span" style="font-weight: bold;">[If...]</span></span></div>
<div>If I change the hdb file as follows,</div><div><br></div><div><span class="Apple-style-span" style="font-family: -webkit-monospace; "><pre style="margin-top: 0em; margin-right: 0em; margin-bottom: 0em; margin-left: 0em; ">
Eth 2
2 6 H1 C1 C2 C1
2 6 H2 C2 C1 C2</pre></span></div><div><br></div><div>After doing pdb2gmx, I got only 12 H-atoms (which means my terminal did NOT work...).</div><div>And those positions are all (0, 0, 0).</div>
<div><br></div><div>Following is the results,</div><div><br></div><div><div>LE Giving Russians Opium May Alter Current Situation</div><div>MODEL 1</div><div>ATOM 1 C1 PEt 1 1.000 0.000 0.000 1.00 0.00</div>
<div>ATOM 2 H11 PEt 1 0.000 0.000 0.000 1.00 0.00</div><div>ATOM 3 H12 PEt 1 0.000 0.000 0.000 1.00 0.00</div><div>ATOM 4 C2 PEt 1 2.450 6.000 1.000 1.00 0.00</div>
<div>ATOM 5 H21 PEt 1 0.000 0.000 0.000 1.00 0.00</div><div>ATOM 6 H22 PEt 1 0.000 0.000 0.000 1.00 0.00</div><div>ATOM 7 C1 PEt 2 2.450 6.000 1.000 1.00 0.00</div>
<div>ATOM 8 H11 PEt 2 0.000 0.000 0.000 1.00 0.00</div><div>ATOM 9 H12 PEt 2 0.000 0.000 0.000 1.00 0.00</div><div>ATOM 10 C2 PEt 2 3.910 2.000 3.000 1.00 0.00</div>
<div>ATOM 11 H21 PEt 2 0.000 0.000 0.000 1.00 0.00</div><div>ATOM 12 H22 PEt 2 0.000 0.000 0.000 1.00 0.00</div><div>ATOM 13 C1 PEt 3 3.910 2.000 3.000 1.00 0.00</div>
<div>ATOM 14 H11 PEt 3 0.000 0.000 0.000 1.00 0.00</div><div>ATOM 15 H12 PEt 3 0.000 0.000 0.000 1.00 0.00</div><div>ATOM 16 C2 PEt 3 5.360 8.000 4.000 1.00 0.00</div>
<div>ATOM 17 H21 PEt 3 0.000 0.000 0.000 1.00 0.00</div><div>ATOM 18 H22 PEt 3 0.000 0.000 0.000 1.00 0.00</div><div>TER</div><div>ENDMDL</div></div><div><br></div><div><span class="Apple-style-span" style="color: rgb(255, 0, 0);"><span class="Apple-style-span" style="font-weight: bold;">[Question #3 from If... section ]</span></span></div>
<div>I guess that I have to change hdb and tdb files.</div><div>Would you please give some guide on that...?</div><div><br></div><div>Thank you for your care!</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 8:35 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 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 could be not that hard to simulate it in Gromacs.<br>
Trying to do, I have read Dr. Benkova's articles in gmx-users 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 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>
</blockquote>
<br></div>
The .hdb file format is explained in the manual.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
[Q2]<br>
When I use -C2, and +C1 in hdb file, I always meet error.<br>
</blockquote>
<br></div>
What is the error?<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">
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></div>
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</blockquote>
<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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