mm...sorry for incorrect explanation of the task. I know how to use index_ndx and g_select, but I don't know whether it is possible to create an index group of all atoms in !!sphere!! with a radius of 10 angstrom around selected "carbon" (for example). Exactly I don't know how and where to determine a sphere's parameters. As you understand if this sphere includes SOL molecules (which are flexible and all time will be changing one to another from outside to the inside of the sphere), so I have to define not atom numbers of SOL but constant spatial character of the sphere. IS IT possible? With a use of index file it will look like a new index.ndx, with [sphere] section and its content, for each frame
------------------------------ > > Message: 4 > Date: Sat, 10 Sep 2011 00:00:23 +0300 > From: ??????? ???????? <rayevsk...@gmail.com> > Subject: [gmx-users] (no subject) > To: gmx-users@gromacs.org > Message-ID: > <CAB6CZ-=eZHExKyUJRBXrxpAAa0zkHxT=apgyae_jh6bne7y...@mail.gmail.com > > > Content-Type: text/plain; charset="koi8-r" > > Hi. I've look through the manual and didn't find an answer on my question: > i've got a trajectory and i want to convert it in *.pdb with such > parameters > of index file [all atoms within a sphere with a chosen radius around > selected atom]. What can i do? Thank you > > > -- > *ó ��������Í! > > > *** > * > > Nemo me impune lacessit* > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110910/3611a8e9/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Fri, 09 Sep 2011 17:02:40 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] (no subject) > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4e6a7ef0.9050...@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > Алексей Раевский wrote: > > Hi. I've look through the manual and didn't find an answer on my > > question: i've got a trajectory and i want to convert it in *.pdb with > > such parameters of index file [all atoms within a sphere with a chosen > > radius around selected atom]. What can i do? Thank you > > > > Use g_select to generate the index group and trjconv to write the file in > the > format (and with the contents) that you want. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > -- *С уважением! *** * Nemo me impune lacessit*
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