<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi all,<div>I am experimenting with Gromacs a little bit and try to open the tpr file and the corresponding trajectory in chimera. Works fine, but the numbering is completely wrong. The residues get numbered continuous and not starting at 1 for the next chain.</div><div>Not sure if the problem is in the tpr file or in chimera.</div><div><br></div><div>I have 4 chains in my pdb file and all have a chain identifier, O P g and h and they are separated by TER</div><div>I have also 4 .itp files with names like “<span style="font-family: Menlo;">topol_Protein_chain_O.itp</span>”</div><div>My topol.top file say 4 molecules</div><div><div style="margin: 0px; font-family: Menlo;">[ molecules ]</div><div style="margin: 0px; font-family: Menlo;">; Compound #mols</div><div style="margin: 0px; font-family: Menlo;">Protein_chain_O 1</div><div style="margin: 0px; font-family: Menlo;">Protein_chain_P 1</div><div style="margin: 0px; font-family: Menlo;">Protein_chain_g 1</div><div style="margin: 0px; font-family: Menlo;">Protein_chain_h 1</div></div><div style="margin: 0px; font-family: Menlo;"><br></div><div style="margin: 0px; font-family: Menlo;">and</div><div style="margin: 0px; font-family: Menlo;"><div style="margin: 0px;">; Include chain topologies</div><div style="margin: 0px;">#include "topol_Protein_chain_O.itp"</div><div style="margin: 0px;">#include "topol_Protein_chain_P.itp"</div><div style="margin: 0px;">#include "topol_Protein_chain_g.itp"</div><div style="margin: 0px;">#include “topol_Protein_chain_h.itp"</div><div style="margin: 0px;"><br></div></div><div style="margin: 0px;">I create my tpr file with grompp </div><div style="margin: 0px;"><br></div><div style="margin: 0px;">Has anybody experience with this kind of issue?</div><div style="margin: 0px;"><br></div><div style="margin: 0px;">Kind regards</div><div style="margin: 0px;">Mario</div></body></html>