[gmx-users] dendrimer simulation

[nemethl at pharm.u-szeged.hu]

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