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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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<p class="MsoNormal"><span style="font-family:"Times New Roman",serif;color:black">Office: +1 (304)-766-5168</span><o:p></o:p></p>
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