[gmx-users] dendrimer simulation

Justin Lemkul jalemkul at vt.edu
Tue Jul 24 16:20:30 CEST 2012

On 7/24/12 10:14 AM, nemethl at pharm.u-szeged.hu wrote:
> 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).

You cannot create bonds between molecules in separate [moleculetype] blocks. 
Thus, if your molecules are in separate .itp files, you cannot create the 
necessary bonds.  For branched molecules, the only way to have such linkages is 
to create .rtp entries and use specbond.dat.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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