<div>Thanks for Mark and Justin's help. But I have new questions as follows:</div>
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<div>CYS SG 1 HEME FE 2 0.25 CYS2 HEME</div>
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<div>1.residue name A<br>2.atom name A<br>3.number of bonds that this atom can form <font color="#cc0000">(does the number include the bonds of atom with H atoms?)</font><br>4.residue name B<br>5.atom name B<br>6.number of bonds that this atom can form<br>
7.the reference length for searching for candidate bonds, the margin is ±10%<font color="#cc0000"> ( It seems the unreasonable length can result in the unexpected bond. does it? )<br></font>8.the new name for residue A <font color="#cc0000">( Why new residue name?)</font><br>
9.the new name for residue B<br></div>
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<div>Thanks again.<br></div>
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<div class="gmail_quote">2010/10/9 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div class="im"><br><br>lammps lammps wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Hi Mark,<br><br>Thanks for your reply. But, I do not know the meaning of the columns in specbonds.dat. I also do not find any information in the manual 4.0.<br>
<br>Could you provide something about the specbonds.dat or give some explanations.<br><br></blockquote><br></div><a href="http://www.gromacs.org/Documentation/File_Formats/specbond.dat" target="_blank">http://www.gromacs.org/Documentation/File_Formats/specbond.dat</a><br>
<br>-Justin<br><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Thanks in advance.<br><br><br><br>2010/10/9 Mark Abraham <<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a> <mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>>>
<div class="im"><br><br><br><br> ----- Original Message -----<br> From: lammps lammps <<a href="mailto:lammp2forum@gmail.com" target="_blank">lammp2forum@gmail.com</a><br></div>
<div class="im"> <mailto:<a href="mailto:lammp2forum@gmail.com" target="_blank">lammp2forum@gmail.com</a>>><br> Date: Saturday, October 9, 2010 19:27<br> Subject: [gmx-users] how to write a rtp file for amido amine<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>
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<div class="h5"> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><br><br> > Hi everybody,<br> ><br> > I want to use pdb2gmx command to create a .gro file and a .top<br>
file for PAMAM whose repeat unit is amidoamine ( attached ).<br> ><br> > /<br> > ---CH2--CH2--CO-NH-CH2-CH2-N (see the attached figure)<br> > \<br>
><br> > The atom N have two same branches with --CH2--. I write the rtp<br> file for it as follows:<br> ><br> > [ atoms ]<br> > C1 opls_245 -0.050 1 > .........<br> > [ bonds ]<br>
> C1 -N7<br> > .......<br> > C6 N7<br> > N7 +C1<br> > N7 +C1<br> ><br> > It seems not work, which gives a wrong top structure. The<br> question is how can I deal with the two branches of N. Any<br>
suggestion is appreciated.<br><br> pdb2gmx is intended only for work with linear heteropolymers. Any<br> more complex things (e.g. disulfides, branched structures) have to<br> be engineered using the specbonds.dat mechanism.<br>
<br> Mark<br> --<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div></div> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>
<div class="im"><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> Please search the archive at<br> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div> <mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.
<div class="im"><br> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br><br><br><br>-- <br>wende<br><br></div></blockquote>
<br>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<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>========================================<br><font color="#888888">-- <br>
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<div class="h5">gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></div></div></blockquote></div><br><br clear="all"><br>-- <br>wende<br>