<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>Hi Justin<br></div><div><br></div><div>You wrote: <br></div><div><br></div><div>>If you do not specify any output file, the default is this .xvg file
that tells you how many atoms satisfied the >criterion specified in the
selection string. If you want a coordinate file, it's a two-step
process.<br>><br>>1. Run g_select using the -on flag to produce an output index file of the atoms that satisfy your criterion.<br>><br>>2. Use trjconv with that index file in and your coordinate file to generate the structure with those atoms.</div><div><br></div>I used the command:<br><br>g_select -s molecule_in_water.pdb -select '"Close to ISO" resname SOL and within 0.5 of resname ISO' -on <br><br>And got the size.xvg file and an index.ndx file. Than I want to make my coordinate file by<br><br>trjconv -n index.ndx<br><br>and got the error<br><br>Can not open file:<br>traj.xtc<br><br>I have no traj.xtc file. <br><br>Thank you for helping me<br><br>Greetings<br>Lara<br><br><br><br><br><span></span><div><br><span></span></div><div><span></span></div><div><br></div> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div
dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">Von:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br> <b><span style="font-weight: bold;">An:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Gesendet:</span></b> 17:27 Samstag, 14.April 2012<br> <b><span style="font-weight: bold;">Betreff:</span></b> Re: [gmx-users] File editing - only one layer of water around a molecule<br> </font> </div> <br><br><br>Lara Bunte wrote:<br>> Hi Justin<br>> <br>> The difference in my<br>> <br>> g_select -s molecule_in_water.pdb -select '"Close to ISO" resname SOL and within 0.5 of group "ISO"'<br>> <br>> and your<br>> <br>> g_select -s molecule_in_water.pdb -select '"Close to ISO" resname SOL and within 0.5 of resname ISO'<br>> <br>> is, that the last ISO is not in quotation marks. Could you please explain?<br>>
<br><br>There is a much greater difference. The first command uses 'group "ISO"' which assumes that there is a group (either generated by default or present in a supplied index file) named "ISO." Apparently this is not the case. What I used was 'resname ISO' which is generic syntax for any residue name that I like (i.e., not a group). You can use it with any residue name in the structure.<br><br>> With your command I got this time no error but I got other stuff that I don't understand:<br>> <br>> 1.)<br>> I got this warnings:<br>> <br>> WARNING: masses and atomic (Van der Waals) radii will be determined<br>> based on residue and atom names. These numbers can deviate<br>> from the correct mass and radius of the atom type.<br>> <br>> <br>> WARNING: if there are broken molecules in the trajectory file,<br>>
they can not be made whole without a run input file<br>> <br>> Can I ignore this or is this serious?<br>> <br><br>These are probably not important. They are generic warnings that many Gromacs programs will produce if they are run without a .tpr file.<br><br>> 2.)<br>> My output is one file called size.xvg. It contains<br>> <br>> # This file was created Sat Apr 14 16:55:56 2012<br>> # by the following command:<br>> # g_select -s molecule_in_water.pdb -select "Close to ISO" resname SOL and within 0.5 of resname ISO<br>> #<br>> # g_select is part of G R O M A C S:<br>> #<br>> # Green Red Orange Magenta Azure Cyan Skyblue<br>> #<br>> @ title "Selection size"<br>> @ xaxis label "Time (ps)"<br>> @ yaxis label "Number"<br>> @TYPE xy<br>> # Selections:<br>> # "Close to ISO" resname SOL and within 0.5 of resname ISO<br>>
#<br>> @ view 0.15, 0.15, 0.75, 0.85<br>> @ legend on<br>> @ legend box on<br>> @ legend loctype view<br>> @ legend 0.78, 0.8<br>> @ legend length 2<br>> @ s0 legend "Close to ISO"<br>> 0.000 848.000<br>> <br>> What is the interpretation of this? What I need is a new pdb. file that has to contain only the molecule ISO and the water layer SOL around it. Is this possible with g_select?<br>> <br><br>If you do not specify any output file, the default is this .xvg file that tells you how many atoms satisfied the criterion specified in the selection string. If you want a coordinate file, it's a two-step process.<br><br>1. Run g_select using the -on flag to produce an output index file of the atoms that satisfy your criterion.<br><br>2. Use trjconv with that index file in and your coordinate file to generate the structure with those atoms.<br><br>-Justin<br><br>> Thanks for helping me.<br>>
Greetings<br>> Lara<br>> <br>> <br>> p.s.<br>> I use yahoo. I tried to find an "answer to all" option or something like that. Again after pressing answer the mail should go only to Justin. I put the mailing list in cc. Is here someone using yahoo also and know how to fix this?<br>> <br>> <br>> <br>> <br>> ------------------------------------------------------------------------<br>> *Von:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *An:* Lara Bunte <<a ymailto="mailto:lara.bunte@yahoo.de" href="mailto:lara.bunte@yahoo.de">lara.bunte@yahoo.de</a>>; Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Gesendet:* 16:56 Samstag, 14.April 2012<br>> *Betreff:* Re: [gmx-users] File editing - only one layer of water around a molecule<br>>
<br>> <br>> <br>> Lara Bunte wrote:<br>> > I still got the problem. What is wrong in this command:<br>> ><br>> > g_select -s molecule_in_water.pdb -select '"Close to ISO" resname SOL and within 0.5 of group "ISO"'<br>> ><br>> > In the pdb. file ISO is for the molecule and SOL for the water.<br>> ><br>> > Please help<br>> ><br>> <br>> The above command assumes "ISO" is a default group, like "Protein" or something else. You can make selections based on any arbitrary residue name with something like the following:<br>> <br>> g_select -s molecule_in_water.pdb -select '"Close to ISO" resname SOL and within 0.5 of resname ISO'<br>> <br>> Does that work?<br>> <br>> -Justin<br>> <br>> -- ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>>
MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>> <br>> ========================================<br>> <br>> <br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a
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