<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Thanks.</span></div><div><span></span> </div><div><span>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. </span></div><div><span></span> </div><div><span>This makes me confused when you define "1-27" to chain A, and "28-54" to chain B.</span></div><div><span></span> </div><div><span>It seems your tutorial protein is a 2 chain protein, not the 5 chain protein.</span></div><div><span></span> </div><div><span>Can you give me further
clarification?</span></div><div><span></span> </div><div><span>Cheers,</span></div><div><span></span> </div><div><span>Acoot</span></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 10:49 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>> Here I also mean how can I get the index.npt in the "grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr".<br>> Looking forward to getting your advice.<br>> <br><br>That file is produced by make_ndx. It is written when you type 'q' and Enter to quit the program. If you have not specified any other output name, the default is "index.ndx."<br><br>-Justin<br><br>> Cheers,<br>> Acoot<br>> <br>> *From:* Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *To:* Acoot Brett <<a href="mailto:acootbrett@yahoo.com" ymailto="mailto:acootbrett@yahoo.com">acootbrett@yahoo.com</a>>; Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Sunday, 1 April 2012 10:32
PM<br>> *Subject:* Re: [gmx-users] on Umbrella Sampling<br>> <br>> <br>> <br>> Acoot Brett wrote:<br>> > Dear All,<br>> > In the on-line tutorial "Umbrella Sampling " by*Justin Lemkul in "<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html</a>"* , there is a command "grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr". Here is the index.ndx exactly same as following?<br>> > make_ndx -f npt.gro<br>> > (> indicates the make_ndx prompt)<br>> > > r 1-27<br>> > > name 19 Chain_A<br>> > > r 28-54<br>> > > name 20 Chain_B<br>> > > q<br>> > Then what is the meaning of "r1-27",
what is the meaning of " name 19 Chain_A", and what is the meaning of "q"?<br>> > <br>> Type "help" at the make_ndx prompt for an explanation.<br>> <br>> > Suppose I have a protein-peptide complex A, the protein is of 400 aas,the peptide is 20 aas. Suppose I have another protein-peptide complx B, and the only difference beteen protein complex A and complex B is that in position 3 of peptide of complex A, it is Ala. In the coresponsing position of the peptide of complex B, it is Arg.<br>> > Can the results of this Umbrella Sampling calculation be accurate enough to show that the binding energy between the protein and peptide in complex A and B is different and cuurently reflects the fact that the difference is caused by the substitution of Ala by Arg?<br>> > <br>> Probably.<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>> <br>> <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"
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