On 7/24/12 10:14 AM, neme...@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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