get it<br><br>Thanks very much!!<br><br><br><br><div class="gmail_quote">2010/10/10 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
lammps lammps wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks for Mark and Justin's help. But I have new questions as follows:<br>
CYS SG 1 HEME FE 2 0.25 CYS2 HEME<br>
1.residue name A<br>
2.atom name A<br>
3.number of bonds that this atom can form (does the number include the bonds of atom with H atoms?)<br>
</blockquote>
<br></div>
It should pertain to the number of bonds you want that atom to form, aside from those in the .rtp entry. See the line for HIS NE2, which forms one bond to FE, but certainly forms other bonds to atoms in the HIS residue.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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% ( It seems the unreasonable length can result in the unexpected bond. does it? )<br>
</blockquote>
<br></div>
I don't understand your question. If you define a bond at, i.e. 0.1 nm, pdb2gmx will build a bond if the distance between the two atoms is 0.9 - 1.1 nm. An unreasonable bond will only be formed if you provide an unreasonable search distance.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
8.the new name for residue A ( Why new residue name?)<br>
</blockquote>
<br></div>
This isn't always relevant. Note that most of the entries in specbond.dat remain unchanged. The only instances of the residue name changing are related to force field-specific disulfide conventions (i.e., CYS vs. CYS2).<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
9.the new name for residue B<br>
Thanks again.<br></div>
2010/10/9 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>>><div class="im"><br>
<br>
<br>
<br>
lammps lammps wrote:<br>
<br>
Hi Mark,<br>
<br>
Thanks for your reply. But, I do not know the meaning of the<br>
columns in specbonds.dat. I also do not find any information<br>
in the manual 4.0.<br>
<br>
Could you provide something about the specbonds.dat or give some<br>
explanations.<br>
<br>
<br>
<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>
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><br></div>
<mailto:<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>
<mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>>>><br>
<br>
<br>
<br>
<br>
----- Original Message -----<br>
From: lammps lammps <<a href="mailto:lammp2forum@gmail.com" target="_blank">lammp2forum@gmail.com</a><br>
<mailto:<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> <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>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br></div><div><div></div><div class="h5">
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <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<br>
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)<br>
have to<br>
be engineered using the specbonds.dat mechanism.<br>
<br>
Mark<br>
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<br>
-- wende<br>
<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></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><div></div><div class="h5"><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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<br>
-- <br>
wende<br>
</div></div></blockquote><div><div></div><div class="h5">
<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>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>wende<br>