Hi Christian, Thank you for the link! We have written a script locally, was wondering if one existed elsewhere though!
Thanks again for your help, Billy On Wed, 13 Nov 2019 at 05:52, Christian Blau <b...@kth.se> wrote: > Hi Billy, > > > I cannot offer a script for the merging of the topologies, but depending > on the transformation you want to carry out, I can suggest using pmx > > http://pmx.mpibpc.mpg.de/webserver.html > > > for preparing dual topologies for alchemical free energy calculations > that are GROMACS-compatible. > > > Best, > > Christian > > On 2019-11-11 07:22, Billy Williams-Noonan wrote: > > Hi Experts, > > > > I have a protein .itp file > > > > I -also- have the dual ligand .itp file to perform a relative alchemical > > transformation > > > > Both are compatible with GROMACS, and use AMBER/GAFF parameters. > > > > I need a script that can easily merge the two together. Have been doing > on > > Excel. I was wondering if anyone would be kind enough to please share? > > > > FESetup is good, but the input requires correct atom naming for Amber > (not > > GROMACS) and this is a pain to get right. > > > > Cheers, > > Billy > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Billy Noonan* | *PhD Student *|* Bsci ( *Adv* ), IA Hon *LinkedIn Profile <http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button> **|* +61420 382 557 Monash Institute for Pharmaceutical Sciences ( *MIPS* ) Royal Parade, Parkville, 3052 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.