Hi,<div><br></div><div>I tried protein protein simulation in gromacs.</div><div><br></div><div>I prepared one ptn and kept seperately with its .top, .itp, .gro files.</div><div><br></div><div>Then I prepared another protein and I build the complex of pasting the .gro file of first processed protein in the .gro file of second processed ptn.</div>
<div><br></div><div>In the topol.top of second protein I included the molecule type at the bottom and inserted</div><div> </div><div> ;Include ligand topology </div><div> #include "posre.itp"</div><div><br>
</div><div>And i run succeccfully the newbox generation, solvent adding commands.</div><div><br></div><div>But with the ions adding command it shows fatal error that the atoms in topol.top and solv.gro is different.</div>
<div><div><font face="courier new, monospace"><br></font></div><div><font face="courier new, monospace">`Fatal error:</font></div><div><font face="courier new, monospace">number of coordinates in coordinate file (solv.gro, 231262)</font></div>
<div><font face="courier new, monospace"> does not match topology (topol.top, 237548)</font></div></div>
<div><br></div><div>on analysing the difference between two files i come to know that it is taking the atoms of first protein for the second protein though i named first and second proteins different.</div><div><br></div>
<div>I changed the residue information in .gro of first file to 1LIG and change everything regarding second molecules name as 1LIG</div><div><br></div><div>and after retrying the ions adding command it says no such molecule type found.</div>
<div><br></div><div><div><font face="courier new, monospace">`Fatal error:</font></div><div><font face="courier new, monospace">No such moleculetype 1LIG</font></div><div><font face="courier new, monospace">For more information and tips for troubleshooting, please check the GROMACS</font></div>
<div><font face="courier new, monospace">website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a></font></div></div><div><br></div><div><br></div><div>
kindly help me to trace where I m doing the mistake and to run ptn ptn simulation.</div>
<div><br></div><div><br></div><div><div><br></div>-- <br>Regards,<div>Rethina.<br><br><font color="#c0c0c0">Rethina Malliga Gunasekaran,<br>Department Of BioInformatics,</font><div><font color="#c0c0c0">Science Block,<br>
Alagappa University,<br>Karaikudi – 630 003, India.</font><br><span style="font-size:13px;font-family:arial,sans-serif"><a href="http://alagappauniversity.academia.edu/RethinamalligaGunasekaran/" style="color:rgb(6,88,181)" target="_blank">http://alagappauniversity.academia.edu/RethinamalligaGunasekaran/</a></span></div>
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