Thank you for the fast answer, i will do that then. Do i have to close this thread, or it will fade by itself?
Lukacs > > > On 7/24/12 10:14 AM, [email protected] 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 > > ======================================== > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
