<div>I was also trying to put more than one protein in one simulation box. I was able to do it with genconf but it appears that the addition is in very ordered manner if one looks .gro file in VMD. How can I add these protein in disordered random orientation.</div>
<div>msnayeem<br><br> </div>
<div><span class="gmail_quote">On 4/20/10, <b class="gmail_sendername">Justin A. Lemkul</b> <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><span class="q"><br><br>fahimeh bafti wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Thanks :)<br>but I couldn't manage with that, it makes the same error with editconf as well, the problem was related to having more than one residue inside insert.gro<br>
</blockquote><br></span>editconf should not have a problem placing multi-residue molecules within a box. That is its main function, so I can only assume you did something wrong.<span class="q"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">I did it at the end with genconf<br><br>genconf -nbox 2 2 2 (as u want) -f file.gro -o file_replicate.pdb<br>
<br>it will simply replicate the unit.<br><br></blockquote><br></span>That works. Glad you found a solution.<br><br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div><span class="e" id="q_1281c28797a4214e_4">Fahimeh<br><br> > Date: Tue, 20 Apr 2010 09:12:44 -0400<br> > From: <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br>
> To: <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br> > Subject: Re: [gmx-users] genbox<br> ><br> ><br> ><br> > fahimeh bafti wrote:<br>
> > Thank you Justin<br> > > but I end up with a new error. now in the insert.pdp file I have a<br> > > molecule which I need to add 4 copy of that inside the solute.pdb<br> > > genbox_d -ci insert.pdb -nmol 4 -cp solute.pdb<br>
> ><br> > > but it gave me:<br> > ><br> > > Fatal error:<br> > > more then one residue in insert molecules<br> > > program terminated<br> > ><br> ><br> > Then you have two options:<br>
><br> > 1. Use the development (git) version of the code, which I believe can now deal<br> > with multi-residue molecules.<br> > 2. Use editconf to position all the components of your system.<br> ><br> > You could, I suppose, hack your "insert.pdb" to contain one residue (i.e.,<br>
> through renaming and renumbering) and then convert it back, but that sounds like<br> > a mess. Probably #2 is the easiest.<br> ><br> > -Justin<br> ><br> > > Fahimeh<br> > ><br> > ><br> > > > Date: Tue, 20 Apr 2010 07:10:59 -0400<br>
> > > From: <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br> > > > To: <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
> > > Subject: Re: [gmx-users] genbox<br> > > ><br> > > ><br> > > ><br> > > > fahimeh bafti<br> > > > > Hello,<br> > > > ><br> > > > > I want to use a file.pdb which has 8 chain of polypeptide, each chain<br>
> > > > contains 6 residues. I need to expand it to 12 chains of 6 rsidues<br> > > so I<br> > > > > need to add 4 chains or in the other word 24 residues. I think I<br> > > have to<br>
> > > > use genbox, so I make another copy of file.pdb and rename it to<br> > > > > insert.pdb and i used this command, but it doesn't work.<br> > > > ><br> > > > > genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro<br>
> > > ><br> > > > > can anybody help me?<br> > > ><br> > > > The implication with genbox -ci -nmol is that the coordinate file<br> > > passed to -ci<br> > > > contains one molecule, and an additional -nmol molecules are<br>
> > inserted. So if<br> > > > you already have 8, you need a coordinate file with one polypeptide<br> > > and then:<br> > > ><br> > > > genbox -ci insert.pdb -nmol 4<br> > > ><br>
> > > Note in the documentation that -nmol refers to the number of<br> > > molecules, not a<br> > > > number of residues, which I think is the root of your problem.<br> > > ><br> > > > -Justin<br>
> > ><br> > > > ><br> > > > > Fahimeh<br> > > > ><br> > > > ><br> > > ------------------------------------------------------------------------<br> > > > > Hotmail: Trusted email with powerful SPAM protection. Sign up now.<br>
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> ><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]<a onclick="return top.js.OpenExtLink(window,event,this)" href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br> > <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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<div><span class="e" id="q_1281c28797a4214e_6"><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]<a onclick="return top.js.OpenExtLink(window,event,this)" href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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