Hi Mark, Thanks for the replay. I actually hold the modified force filed files in the same directory in which I simulate, less mess in the system.
Cheers, Itamar -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut =========================================== | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@med.monash.edu.au ============================================ ----- Original Message ----- From: Mark Abraham <mark.abra...@anu.edu.au> Date: Tuesday, February 16, 2010 4:51 pm Subject: Re: [gmx-users] indexing and new molecules To: Discussion list for GROMACS users <gmx-users@gromacs.org> <div style="font-family: 'Times New Roman'; font-size: 16px;"><br /><br /><span>On 02/16/10, <b class="name">Itamar Kass </b> <itamar.k...@med.monash.edu.au> wrote:</span><blockquote cite="mid:f56c5a6a5807.5807f56c5...@monash.edu.au" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text plain">Shalom all,<br /><br />I am simulating a protein in which one of the residues is chemically<br />modified (non-natural) - so I had to add it into aminoacids.dat.<br /><br />I found that when I analyse my results, and use the index group of the<br />protein this amino acid does not count unless the aminoacids.dat file is<br />available in the same folder.</div></blockquote><br _moz_dirty="" />Such files are searched for first in the local directory and then in $GMXLIB. So if you've used "source /path/to/GMXRC" correctly and modified the corresponding file, you'll be fine. If you have mu ltiple installations, or multiple machines, you need to take some care, of course.<br _moz_dirty="" /><br _moz_dirty="" /><blockquote cite="mid:f56c5a6a5807.5807f56c5...@monash.edu.au" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"></blockquote><blockquote cite="mid:f56c5a6a5807.5807f56c5...@monash.edu.au" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text plain">Now, I don't think this is a bug - it is perfectly logic that in order<br />to index the protein the program needs to know how amino acid looks<br />like. I just think this should be written somewhere.</div></blockquote>Sure. There's a manual section that discusses a small number of the environment variables that GROMACS uses, but I don't know if this tidbit is there. It is not easy to write this information somewhere where it will come to people's attention whene ver it is needed.<br _moz_dirty="" /><br _moz_dirty="" />Mark<br _moz_dirty="" type="_moz" /></div>
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