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

On Sat, February 6, 2010 at 11:08:30 AM, Antoine Delmotte wrote: > Thank you very much for this, Bruce. It will help me, for sure. > > Could you just let me know where you found the parameters or how you generated them? Most of the parameters came from the entry for threonine in ffoplsaa.rtp

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

Thank you very much Fairuz. I will try this. Le 6/02/2010 1:20, fairuz zulkifli a écrit : to create itp file with OPLS force feild, you can try use GAMESS. -fairuz- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

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

Thank you very much for this, Bruce. It will help me, for sure. Could you just let me know where you found the parameters or how you generated them? Thanks in advance. Regards, Antoine Le 5/02/2010 22:39, Bruce D. Ray a écrit : On Fri, February 5, 2010 at 1:06:34 PM, Antoine Delmotte wro

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

Thank you very much for your quick response, Justin. I guess I need a little bit more practise to make the parametrization myself. Do you have any clues on where I could find published parameters? Are there databases for this or something similar? Regards, Antoine Le 5/02/2010 18:23, Justi

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

Antoine Delmotte wrote: Thank you very much for your quick response, Justin. I guess I need a little bit more practise to make the parametrization myself. Do you have any clues on where I could find published parameters? Are there databases for this or something similar? Literature sear

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

to create itp file with OPLS force feild, you can try use GAMESS. -fairuz- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to t

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

On Fri, February 5, 2010 at 1:06:34 PM, Antoine Delmotte wrote: > 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 Gromo

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

Antoine Delmotte wrote: 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,

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

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 OPL