[gmx-users] dendrimer simulation

nemethl at pharm.u-szeged.hu nemethl at pharm.u-szeged.hu
Tue Jul 24 16:39:39 CEST 2012

Thank you for the fast answer, i will do that then. Do i have to close
this thread, or it will fade by itself?

> 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
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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