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 <[email protected]>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 > <[email protected]><[email protected]> > * 写道： > > > 发件人: David van der Spoel <[email protected]> <[email protected]> > 主题: Re: [gmx-users] .top to .itp file conversion > 收件人: "Discussion list for GROMACS users" > <[email protected]><[email protected]> > 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. > [email protected]<http://cn.mc156.mail.yahoo.com/mc/[email protected]> > http://folding.bmc.uu.se > -- > gmx-users mailing list > [email protected]<http://cn.mc156.mail.yahoo.com/mc/[email protected]> > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to > [email protected]<http://cn.mc156.mail.yahoo.com/mc/[email protected]> > . > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- 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
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
