in windows , I use ultraedit, in linux ,use vi
--- 12年6月3日，周日, Justin A. Lemkul <jalem...@vt.edu> 写道： 发件人: Justin A. Lemkul <jalem...@vt.edu> 主题: Re: [gmx-users] Atomtype 1 收件人: "Discussion list for GROMACS users" <gmx-users@gromacs.org> 日期: 2012年6月3日,周日,下午9:19 On 6/3/12 9:16 AM, xi zhao wrote: > > I use Ultraedit to produce new part and paste the files; we add a residue name > and corresponding atom type and interaction parameters > Having never used a commercial text editor, I don't know if its integrity. What happens if you use a different editor, like vi/emacs (Linux/Mac) or Notepad (Windows)? What operating system are you using? The only times I've had pdb2gmx die when reading atom types are when the line endings are bad, so I would strongly suspect this is your issue. -Justin > 4 > <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844> > > --- *12年6月3日，周日, Justin A. Lemkul /<jalem...@vt.edu>/* 写道： > > > 发件人: Justin A. Lemkul <jalem...@vt.edu> > 主题: Re: [gmx-users] Atomtype 1 > 收件人: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > 日期: 2012年6月3日,周日,下午8:46 > > > > On 6/3/12 8:24 AM, xi zhao wrote: > > Dear gmx-users: > > I add a new residue in *rtp ,according to > > > >http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, > > and modified corresponding files :such as atp, hdb , after making a >full > copy of > > the installed forcefield in woring diectory. > > When pdb2gmx_d > > appeared " > > All occupancies are one > > Opening force field file ./amber99sbr.ff/atomtypes.atp > > Atomtype 1" > > Please give me suggestions > > Did the program hang here? Did it crash? What modifications did you make, > and to what files? Are you using a plain text editor that properly treats > newlines? > > -Justin > > -- ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- gmx-users mailing list gmx-users@gromacs.org > <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org> > 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 gmx-users-requ...@gromacs.org > ><http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
