I have to simulate a G0 PAMAM dendrimer, functionalized on the 4 hands with peptide oligomers. I have succesfully generated the .itp file needed, and have run some simulation. The same applies to the peptide. However i run into problems combining them. It appears the specbond.dat file is only applied when invoking pdb2gmx, but my dendrimer is not added to the .rtp database, so pdb2gmx fails. (The peptide is bonded through a disulfide like bond to the dendrimer.) Is there an option to directly linking the denrimer and the peptide in the topology files? (the dendrimer utilises GAFF parameters, and they are only present in the .itp file, i dont especialy want to extend the regular force field with these parameters).
Any suggestions are appreciated Lekacs Nemeth -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
