<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>I have not read your original article. Maybe I will read it tomorrow. </span></div><div><span></span> </div><div><span>But the original pdb file has 5 same chains, and from your tutorial it seems you pdb file for the tutorial has 2 different chains. Will you please let me know how do you get you pdb file for your tutorial/ Or you just have 1 chain in your tutorial PDB file, but in the gro file you defined it into 2 chains from a single chain?</span></div><div><span></span> </div><div><span>Cheers,</span></div><div><span></span> </div><div><span>Acoot</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 size="2" face="Arial"> <div
style="margin: 5px 0px; padding: 0px; border: 1px solid rgb(204, 204, 204); height: 0px; line-height: 0; font-size: 0px;" class="hr" contentEditable="false" readonly="true"></div> <b><span style="font-weight: bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Sunday, 1 April 2012 11:04 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] on Umbrella Sampling<br> </font> </div> <br><br><br>Acoot Brett wrote:<br>> Thanks.<br>> The original PDB file (2BEG) has 5 chains. In your tutorial you fix chain B. Thus if I am right, the energy calculated should be the disintegation energy of the whole protein to the 5 chain peptide. In addition the protein chain in the original pdb is from residue 17 to 42.<br>> This makes me
confused when you define "1-27" to chain A, and "28-54" to chain B.<br>> It seems your tutorial protein is a 2 chain protein, not the 5 chain protein.<br>> Can you give me further clarification?<br>> <br><br>The .gro file is renumbered during pdb2gmx.<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>-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
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