<div dir="ltr">Hi Justin,<br>I tried the genpr for generating the posre.itp, but it is taking only a single residue while I want to restrict a number of residue for the mdrun.<br>Please suggest me the way out.<br><br>Procedure followed:<br>
....generated gro using pdb2gmx<br>....generated box using editconf<br>....add water using genbox<br>....make pr.index file for the residues I want to restrict for MDS (for say 10 residues)<br>....tried genpr command to generate the posre.itp using pr.index generated above.<br>
In th elast step it is generating the posre.itp for a single residue and not allowing to include more residues..<br>as r_26 in following response..while I want to select all of r_27,28 and 29<br><br><br>Select group to position restrain<br>
Group 0 ( System) has 23342 elements<br>Group 1 ( Protein) has 2626 elements<br>Group 2 ( Protein-H) has 2073 elements<br>Group 3 ( C-alpha) has 269 elements<br>Group 4 ( Backbone) has 807 elements<br>
Group 5 ( MainChain) has 1077 elements<br>Group 6 (MainChain+Cb) has 1329 elements<br>Group 7 ( MainChain+H) has 1342 elements<br>Group 8 ( SideChain) has 1284 elements<br>Group 9 ( SideChain-H) has 996 elements<br>
Group 10 ( Prot-Masses) has 2626 elements<br>Group 11 ( Non-Protein) has 20716 elements<br>Group 12 ( NDP) has 61 elements<br>Group 13 ( SOL) has 20655 elements<br>Group 14 ( Other) has 20716 elements<br>
Group 15 ( r_25) has 5 elements<br>Group 16 ( r_26) has 9 elements<br>Group 17 ( r_27) has 5 elements<br>Group 18 ( r_28) has 17 elements<br>Group 19 ( r_29) has 10 elements<br>
Select a group: pr<br>Error: Multiple groups 'pr' selected<br>Error: No such group 'pr'<br>Select a group: 16<br>Selected 16: 'r_26'<br><br>Back Off! I just backed up posre.itp to ./#posre.itp.3#<br>
<br>gcq#232: "These are Ideas, They are Not Lies" (Magnapop)<br>_____________________________________________________________<br><br>Please suggest<br><br>With Thanks,<br>Vivek<br><br><div class="gmail_quote">2008/10/10 Samuel Coulbourn Flores 花山 <span dir="ltr"><<a href="mailto:scflores@stanford.edu">scflores@stanford.edu</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div style="">You might want to try Simbody (<a href="http://simtk.org" target="_blank">simtk.org</a>). This will allow you to rigidify any part or parts of the molecule you choose. As a bonus, you will not spend resources computing intramolecular interactions in the rigidified regions. <div>
<br></div><div>Sam</div><div><br><div><div><div></div><div class="Wj3C7c">On Oct 10, 2008, at 6:10 AM, Justin A. Lemkul wrote:<br></div></div><blockquote type="cite"><div><div></div><div class="Wj3C7c"><br><br>vivek sharma wrote:<br>
<blockquote type="cite">Hi justin,<br></blockquote><blockquote type="cite">My apologies for asking you so many small queries.<br></blockquote><blockquote type="cite">Can you suggest any good tutorial or reference that talks about this issue of running MD over a selected part of molecule.<br>
</blockquote><br>If you're using PR, all you're doing is position-restrained dynamics.<br><br>-Justin<br><br><blockquote type="cite">With Thanks,<br></blockquote><blockquote type="cite">Vivek<br></blockquote><blockquote type="cite">
2008/10/10 vivek sharma <<a href="mailto:viveksharma.iitb@gmail.com" target="_blank">viveksharma.iitb@gmail.com</a> <<a href="mailto:viveksharma.iitb@gmail.com" target="_blank">mailto:viveksharma.iitb@gmail.com</a>>><br>
</blockquote><blockquote type="cite"> hI justin,<br></blockquote><blockquote type="cite"> Thanks for your response.<br></blockquote><blockquote type="cite"> do I need to specify the index file(for residue that I want to keep<br>
</blockquote><blockquote type="cite"> fix during MD) during GROMPP or just including the psre.itp in<br></blockquote><blockquote type="cite"> topology is enough for the purpose ?<br></blockquote><blockquote type="cite">
With Thanks,<br></blockquote><blockquote type="cite"> Vivek<br></blockquote><blockquote type="cite"> 2008/10/10 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <<a href="mailto:jalemkul@vt.edu" target="_blank">mailto:jalemkul@vt.edu</a>>><br>
</blockquote><blockquote type="cite"> Justin A. Lemkul wrote:<br></blockquote><blockquote type="cite"> vivek sharma wrote:<br></blockquote><blockquote type="cite"> Thanks Justin,<br></blockquote>
<blockquote type="cite"> My goal is to keep certain part fixed and move only a<br></blockquote><blockquote type="cite"> few of the residues (case is like providing flexibility<br></blockquote>
<blockquote type="cite"> to the site of interest only).<br></blockquote><blockquote type="cite"> SO , do I need to specify the residue using some index<br></blockquote><blockquote type="cite">
file ?<br></blockquote><blockquote type="cite"> or is there some other way to specify the part of<br></blockquote><blockquote type="cite"> molecule for position restraining ??<br>
</blockquote><blockquote type="cite"> Make an index file with the residues you want to keep fixed, and<br></blockquote><blockquote type="cite"> pass it<br></blockquote><blockquote type="cite"> to genpr to generate a new posre.itp that corresponds to those<br>
</blockquote><blockquote type="cite"> residues.<br></blockquote><blockquote type="cite"> -Justin<br></blockquote><blockquote type="cite"> With Thanks,<br></blockquote><blockquote type="cite"> Vivek<br>
</blockquote><blockquote type="cite"> 2008/10/10 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></blockquote><blockquote type="cite"> <<a href="mailto:jalemkul@vt.edu" target="_blank">mailto:jalemkul@vt.edu</a>> <<a href="mailto:jalemkul@vt.edu" target="_blank">mailto:jalemkul@vt.edu</a><br>
</blockquote><blockquote type="cite"> <<a href="mailto:jalemkul@vt.edu" target="_blank">mailto:jalemkul@vt.edu</a>>>><br></blockquote><blockquote type="cite"> vivek sharma wrote:<br>
</blockquote><blockquote type="cite"> Hi there,<br></blockquote><blockquote type="cite"> I want to run MD over a part of my molecule ,<br></blockquote><blockquote type="cite"> for few residues<br>
</blockquote><blockquote type="cite"> only (not the whole molecule).<br></blockquote><blockquote type="cite"> Can I do it using GROMACS ?<br></blockquote><blockquote type="cite">
I searched for the online documentation and<br></blockquote><blockquote type="cite"> mailing list, but<br></blockquote><blockquote type="cite"> unable to get appropriate information.<br>
</blockquote><blockquote type="cite"> If somebody has already tried such things<br></blockquote><blockquote type="cite"> earlier, please<br></blockquote><blockquote type="cite"> suggest and direct me for appropriate link and<br>
</blockquote><blockquote type="cite"> address.<br></blockquote><blockquote type="cite"> Well, if your goal is to keep certain parts fixed and<br></blockquote><blockquote type="cite"> allow others<br>
</blockquote><blockquote type="cite"> to move, probably the easiest way to do it is to<br></blockquote><blockquote type="cite"> apply position<br></blockquote><blockquote type="cite"> restraints to the "fixed" part.<br>
</blockquote><blockquote type="cite"> -Justin<br></blockquote><blockquote type="cite"> With Thanks,<br></blockquote><blockquote type="cite"> Vivek<br></blockquote>
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<div><font face="'Hiragino Maru Gothic Pro'" size="4"><span style="font-size: 15px;">Samuel Coulbourn Flores, PhD</span></font></div><div><font face="'Hiragino Maru Gothic Pro'" size="4"><span style="font-size: 15px;">Altman Lab</span></font></div>
<div><font face="'Hiragino Maru Gothic Pro'" size="4"><span style="font-size: 15px;">Department of BioEngineering</span></font></div><div><font face="'Hiragino Maru Gothic Pro'" size="4"><span style="font-size: 15px;">Stanford University</span></font></div>
<div><font face="'Hiragino Maru Gothic Pro'" size="4"><span style="font-size: 15px;"><a href="mailto:samuel.flores@aya.yale.edu" target="_blank">samuel.flores@aya.yale.edu</a></span></font></div><div><font face="'Hiragino Maru Gothic Pro'" size="4"><span style="font-size: 15px;">650.644.8416</span></font></div>
<div><font face="'Hiragino Maru Gothic Pro'" size="4"><span style="font-size: 15px;"><br></span></font></div><div><span style="font-size: 15px;">花山</span></div><div><span style="font-size: 15px;">科学���</span></div><div>
<font face="'Hiragino Maru Gothic Pro'" size="4"><span style="font-size: 15px;">生物工学部</span></font></div><div><font face="'Hiragino Maru Gothic Pro'" size="4"><span style="font-size: 15px;">スタンフォ一ド大学</span></font></div>
<div><font face="'Hiragino Maru Gothic Pro'" size="4"><span style="font-size: 15px;">スタンフォ一ド・髟阡�<span style="font-family: Helvetica; font-size: 12px; white-space: normal;"><span style="font-size: 15px;">カリフォルニウ髟阡察���米国</span></span></span></font></div>
<div><br></div><div><br></div></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div>
</span><br></div></span><br></div></span><br></div></span><br> </div><br></div></div></blockquote></div><br></div>