<div>Thank you for your answer.</div>
<div> </div>
<div>If I am looking at the PDB standard format and my file, I observe that I have only one number between the type of residue and coordinates, and I suppose it is the residue current number. I am indeed missing the chain identifier code, which should be of A1 Fortran format, which I don't really understand (one carachter, but I have 32 chains, so it should be minimum A2 or I2). That I could introduce.</div>
<div>In my pdb entries I dont define any connectors. Should they be a dummy atom, with the corresponding bond, angle, dihedhral, which after that I redefine in the tdb file?</div>
<div>I dont think it is a visualisation artefact, because it really gives less number of bonds, corresponding to the missing intermonomeric bonds.</div>
<div> </div>
<div>Should I do now both (introducing a chain identifier in the pdb, but how?, and defining the intermonomeric bonds via dummy in the pdb and tdb?)?</div>
<div> </div>
<div>Thanks again for your help.</div>
<div> </div>
<div>Best regards,</div>
<div>Andrea<br></div>
<div class="gmail_quote">2008/10/22 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div>
<div></div>
<div class="Wj3C7c">Andrea Muntean wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">I have a *pdb file for a polymer box which I want to use. I defined the residues (the first, the last and the inner monomers).<br>
Pdb2gmx runs, but I obtain a "soup" of monomers instead of N chains a M monomers each.<br>My problem now is how to connect the monomers. What is the best way to do so?<br></blockquote><br></div></div>We can't tell yet. You might have a PDB file with each residue in its own chain. You might have defined residue topologies without suitable connectors. You might be observing a visualization artefact. You might have some warnings from pdb2gmx you haven't observed yet.<br>
<br>Mark<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
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