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Dear gmx-users,<br><br>I would like to simulate the CDK9 protein (3BLH in PDB), but there is one residue (TPO, phosphothreonine), which Gromacs does not recognise.<br><br>I found the PRODRG website as well as force field parameters for TPO for the Gromos96.1 force field. However, I would like to use the OPLS-AA force field. I therefore need a topology file for this force field, which cannot be provided by PRODRG (only useful for united atoms force fields).<br><br>Does anyone have an idea about where I could get the phosphothreonine itp file for OPLS force field?<br><br>Otherwise, could someone give me clues or the link to a good tutorial about how to create this itp file myself? <br><br>Molecular dynamics is something completely new for me so, sorry if I ask stupid questions. It also seems I am not the first one to have this problem but I could not find any solution on the archive of the mailing list.<br><br>I thank you in advance.<br><br>Best regards,<br><br>Antoine<br><br><br> <br /><hr />Hotmail : une messagerie fiable avec la protection anti-spam performante de Microsoft <a href='https://signup.live.com/signup.aspx?id=60969' target='_new'>Inscrivez-vous</a></body>
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