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<div class="moz-cite-prefix">Hello,<br>
<br>
it is better to ask this stuff at the forum (gromacs.bioexcel.eu)
now and maybe repeat the question there, or check if there are
similar questions already.<br>
<br>
This list is only for things related to the GROMACS software
development :)<br>
<br>
If you think that the behavior you describe is a bug, please check
the open issues here (<a class="moz-txt-link-freetext" href="https://gitlab.com/gromacs/gromacs/-/issues">https://gitlab.com/gromacs/gromacs/-/issues</a>)
if something similar has already been filed and if not open a new
issue for it.<br>
<br>
Cheers<br>
<br>
Paul<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">On 23/08/2020 12:53, Sridhar Acharya
Malkaram wrote:<br>
</div>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"
style="mso-margin-bottom-alt:auto;background:white"><span
style="font-size:11.5pt;font-family:Helvetica;color:#222222">Hi
gmx-developers,</span><span
style="font-family:"-webkit-standard",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"
style="mso-margin-bottom-alt:auto;background:white"><span
style="font-size:11.5pt;font-family:Helvetica;color:#222222">I
had originally posted this in the general mailing list, but
without responses. I thought I might get a suggestion here.
Any suggestion is appreciated.</span><span
style="font-family:"-webkit-standard",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"
style="mso-margin-bottom-alt:auto;background:white"><span
style="font-size:11.5pt;font-family:Helvetica;color:#222222">GROMACS version:
2020.3<br>
GROMACS modification: No</span><span
style="font-family:"-webkit-standard",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"
style="mso-margin-bottom-alt:auto;background:white"><span
style="font-size:11.5pt;font-family:Helvetica;color:#222222">I
am working on a scripted run of gromacs energy calculation
(using gmx energy), to calculate energies for specific
groups. I will be specifying in the energygrps option of the
mdp to achieve this. However, I find a problem. The original
residue numbers and chain names are no longer retained after
the series of gromacscommands before the gmx energy
command. </span><span
style="font-family:"-webkit-standard",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;background:white"><span
style="font-size:11.5pt;font-family:Helvetica;color:#222222">I
am using “.pdb” as the input and output structure format for
my simulation to retain the chain name.</span><span
style="font-family:"-webkit-standard",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;background:white"><span
style="font-size:11.5pt;font-family:Helvetica;color:#222222">Gromacs retains
the chain information in output “.pdb” structures for many
of its commands, but when I run mdrun, the output structure
file “.pdb” (the option -c) has lost all chain information.
I checked for any options that can be used to preserve chain
information, but I found none.</span><span
style="font-family:"-webkit-standard",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;background:white"><span
style="font-size:11.5pt;font-family:Helvetica;color:#222222">I
needed chain information in pdb format structure file, to
properly generate index groups.</span><span
style="font-family:"-webkit-standard",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;background:white"><span
style="font-size:11.5pt;font-family:Helvetica;color:#222222">Is
there a way to preserve chain information?</span><span
style="font-family:"-webkit-standard",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;background:white"><span
style="font-size:11.5pt;font-family:Helvetica;color:#222222">Also,
is there a way to prevent residue renumbering ? (Atom
renumbering is not an issue)</span><span
style="font-family:"-webkit-standard",serif;color:black"><o:p></o:p></span></p>
<div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:black">With Kind
Regards,</span><span
style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Sridhar</span><span
style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> </span><span
style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times
New Roman",serif;color:black">Sridhar A Malkaram,
Ph.D.</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times
New Roman",serif;color:black">Associate
Professor,</span><span
style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times
New Roman",serif;color:black">Department of
Mathematics and Computer Sciences</span><span
style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times
New Roman",serif;color:black">W729, Wallace Hall,</span><span
style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times
New Roman",serif;color:black">West Virginia State
University,</span><span
style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times
New Roman",serif;color:black">Institute, WV-25112</span><span
style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
</div>
</div>
<p class="MsoNormal"><span style="font-family:"Times New
Roman",serif;color:black">Office: +1 (304)-766-5168</span><o:p></o:p></p>
</div>
<br>
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<p><br>
</p>
<pre class="moz-signature" cols="72">--
Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594</pre>
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