Hi,<br><br>You can print the moleculetype definition, up to the system tag using sed:<br><br>sed -n -e '/^\s*\[\s*system\s*\]\s*$/q' -e '/^\s*\[\s*moleculetype\s*\]\s*$/,$p' TOP > ITP<br><br>First expression: quit at [ system ], allowing spaces before, in between and after<br>
Second expression: print everything from [ moleculetype ] to end of file.<br><br>This does assume there is only a single moleculetype definition and no rubbish (#includes) in between.<br><br>Hope it helps,<br><br>Tsjerk<br>
<br><div class="gmail_quote">On Mon, Nov 28, 2011 at 12:22 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div text="#000000" bgcolor="#FFFFFF"><div class="im">
On 28/11/2011 10:09 PM, yp sun wrote:
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<td style="font: inherit;" valign="top">I think by running
pdb2gmx you can get .itp file.<br>
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... only if there are corresponding .rtp entries, which is likely
not the case for GTP. pdb2gmx is not magic.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div><div class="h5"><br>
<br>
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<td style="font: inherit;" valign="top"><br>
Yeping Sun<br>
CAS Key Laboratory of Pathogenic Microbiology &
Immunology<br>
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES <br>
NO.1 Beichen West Road,Chaoyang District,Beijing
100101,china<br>
<br>
--- <b>11年11月28日，周一, David van der Spoel <i><a href="mailto:spoel@xray.bmc.uu.se" target="_blank"><spoel@xray.bmc.uu.se></a></i></b>
写道：<br>
<blockquote style="border-left: 2px solid rgb(16, 16, 255); padding-left: 5px; margin-left: 5px;"><br>
发件人: David van der Spoel <a href="mailto:spoel@xray.bmc.uu.se" target="_blank"><spoel@xray.bmc.uu.se></a><br>
主题: Re: [gmx-users] .top to .itp file conversion<br>
收件人: "Discussion list for GROMACS users"
<a href="mailto:gmx-users@gromacs.org" target="_blank"><gmx-users@gromacs.org></a><br>
日期: 2011年11月28日,周一,下午4:22<br>
<br>
<div>On 2011-11-28 09:20, neeru sharma
wrote:<br>
> Dear gromacs users,<br>
><br>
> I have generated Amber topology and coordinate
files for GTP molecule.<br>
> Then, I converted them into the corresponding
gromacs topology (.top)<br>
> and coordinate files (.gro). Now, I need to
convert this gromacs .top<br>
> file into .itp format.<br>
> Is there any command in gromacs or any other tool
to do so.<br>
> Thanks<br>
><br>
> ----<br>
> Neeru Sharma<br>
> CDAC,Pune (India)<br>
><br>
><br>
><br>
emacs or vi. your choice.<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone:
<a href="tel:%2B46184714205" value="+46184714205" target="_blank">+46184714205</a>.<br>
<a href="http://cn.mc156.mail.yahoo.com/mc/compose?to=spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>
<a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se</a><br>
-- <br>
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</div>
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<br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">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<br>
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Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br><br clear="all"><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br>
<br>post-doctoral researcher<br>Molecular Dynamics Group<br>* Groningen Institute for Biomolecular Research and Biotechnology<br>* Zernike Institute for Advanced Materials<br>University of Groningen<br>The Netherlands<br>