[gmx-users] Topology file for phosphothreonine (TPO) for OPLS force field

[Antoine Delmotte]

Dear gmx-users,

I would like to simulate the CDK9 protein (3BLH in PDB), but there is one residue (TPO, phosphothreonine), which Gromacs does not recognise.

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).

Does anyone have an idea about where I could get the phosphothreonine itp file for OPLS force field?

Otherwise, could someone give me clues or the link to a good tutorial about how to create this itp file myself? 

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.

I thank you in advance.

Best regards,

Antoine


 		 	   		  
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