[gmx-users] .top to .itp file conversion

[Tsjerk Wassenaar]

Hi,

You can print the moleculetype definition, up to the system tag using sed:

sed -n -e '/^\s*\[\s*system\s*\]\s*$/q' -e
'/^\s*\[\s*moleculetype\s*\]\s*$/,$p' TOP > ITP

First expression: quit at [ system ], allowing spaces before, in between
and after
Second expression: print everything from [ moleculetype ] to end of file.

This does assume there is only a single moleculetype definition and no
rubbish (#includes) in between.

Hope it helps,

Tsjerk

On Mon, Nov 28, 2011 at 12:22 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 28/11/2011 10:09 PM, yp sun wrote:
>
>   I think by running pdb2gmx you can get .itp file.
>
>
> ... only if there are corresponding .rtp entries, which is likely not the
> case for GTP. pdb2gmx is not magic.
>
> Mark
>
>
>
> Yeping Sun
> CAS Key Laboratory of Pathogenic Microbiology & Immunology
> INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
> NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china
>
> --- *11年11月28日，周一, David van der Spoel <spoel at xray.bmc.uu.se><spoel at xray.bmc.uu.se>
> * 写道：
>
>
> 发件人: David van der Spoel <spoel at xray.bmc.uu.se> <spoel at xray.bmc.uu.se>
> 主题: Re: [gmx-users] .top to .itp file conversion
> 收件人: "Discussion list for GROMACS users" <gmx-users at gromacs.org><gmx-users at gromacs.org>
> 日期: 2011年11月28日,周一,下午4:22
>
> On 2011-11-28 09:20, neeru sharma wrote:
> > Dear gromacs users,
> >
> > I have generated Amber topology and coordinate files for GTP molecule.
> > Then, I converted them into the corresponding gromacs topology (.top)
> > and coordinate files (.gro). Now, I need to convert this gromacs .top
> > file into .itp format.
> > Is there any command in gromacs or any other tool to do so.
> > Thanks
> >
> > ----
> > Neeru Sharma
> > CDAC,Pune (India)
> >
> >
> >
> emacs or vi. your choice.
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
> spoel at xray.bmc.uu.se<http://cn.mc156.mail.yahoo.com/mc/compose?to=spoel@xray.bmc.uu.se>
>   http://folding.bmc.uu.se
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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