Hi Alok,<br><br> Thanks for your email. <br><br> Could you please explain in more detail? What do you mean by chain identifier?<br><br> Many thanks.<br><br>Best regards,<br>Huey Ling<br><br><div><span class="gmail_quote">
On 26/10/2007, <b class="gmail_sendername"><a href="mailto:alokjain@iitk.ac.in">alokjain@iitk.ac.in</a></b> <<a href="mailto:alokjain@iitk.ac.in">alokjain@iitk.ac.in</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello Huey Ling,<br><br>Use different chain identifiers for different peptides.<br><br>Then pdb2gmx will not create any bond between them.<br><br>Regards,<br>Alok<br><br><br>> Hi All,<br>><br>> I am trying to put 2 identical peptide chains in a simulation box.
<br>> However, gromacs tends to see both separate peptide chains as one.<br>><br>> The following is the method that I used, please comment and correct me<br>> if<br>> I'm wrong.<br>><br>> First, I translate the peptide to a certain distance. Then I put the
<br>> .gro<br>> files of the translated peptide in the first .gro file. Later, I change<br>> the<br>> number of the residues and atoms of the second peptide accordingly and<br>> manually.<br>><br>> With the .gro file of the 2 peptide chains, I convert it to pdb file.
<br>> And<br>> then, I use the pdb2mgx to convert the 2peptide.pdb to 2peptide.gro to<br>> generate topology file. The rest of the methods are the conventional<br>> gromacs<br>> simulations such as energy minimisation and position restrained.
<br>><br>> However, gromacs see the 2peptide.pdb file as a file for 1 single<br>> molecule, (not 2 identical peptide chains in a file) and bond is created<br>> between this 2 chains. I tried to use -nmol to insert the second peptide
<br>> in<br>> but that doesn't work. I wonder if anyone have done similar work like mine<br>> before, and willing to share the method with me? Any other suggestion and<br>> comments are most welcome.<br>>
<br>> Many thanks.<br>><br>><br>> --<br>> Best regards,<br>> Huey Ling<br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
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