[gmx-users] costu, fragment force field
I'm attempting to build a costume fragment library of beta amino acids with GAFF parametrization. I have converted the AMBER assigned parameters with acpype, built my .rtp .atp and .itp files. Everything works fine, until grompp, there i get a lot of No default Ryckaert-Bell. types errors. The problem is, that the dihedrals in question are mentioned in the ffbonded.itp file, but the atomtypes are not in good order. How do i figure out the RB parameters for these bonds, in the precise order? Is there a way to convert the parameters to the desired order? Thank you in advance! Lukacs Nemeth -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] dendrimer simulation
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 -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] dendrimer simulation
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, 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 -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
