[gmx-users] Topology file for phosphothreonine (TPO) for OPLS force field
antoinedelmotte at hotmail.com
Fri Feb 5 19:06:34 CET 2010
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.
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