[gmx-users] indexing and new molecules

[Itamar Kass]

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.Kass at med.monash.edu.au
============================================

----- Original Message -----
From: Mark Abraham <mark.abraham at 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 at 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>
&lt;Itamar.Kass at med.monash.edu.au&gt; wrote:</span><blockquote
cite="mid:f56c5a6a5807.5807f56c5a6a at 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
&quot;source /path/to/GMXRC&quot; 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:f56c5a6a5807.5807f56c5a6a at 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:f56c5a6a5807.5807f56c5a6a at 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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