UFF and ReaxFF force fields do not require creation of new parameters for carbohydrates.
Google UFF and ReaxFF to find code that uses them. I know LAMMPS can use ReaxFF and other force fields http://lammps.sandia.gov/ MCCCS Towhee can use UFF and other force fields http://towhee.sourceforge.net/forcefields/uff.html BUFF: A Biological Universal Forcefield Derived from Quantum Mechanics http://www.wag.caltech.edu/publications/theses/mjc/mjc.thesis.htm You might also want to take a look at DL_POLY http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/ There are other as well but this should give you at starting point. Jim > -----Original Message----- > From: gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Nancy > Sent: Friday, July 31, 2009 5:19 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Carbohydrate MD Simulation > > If it necessary to manually create force field parameters for > each molecule, then how can one run a simulation involving a > number of arbitrary molecules (e.g. a set of mono and > disaccharides) for which there are no existing force fields? > > Do you know of any other MD software package that is capable > of running simulations on arbitrary molecules without having > to "piece together" a force field for each molecule? > > Thanks, > > Nancy > > > > > > On Fri, Jul 31, 2009 at 4:53 PM, Justin A. Lemkul > <jalem...@vt.edu> wrote: > > > > > Nancy wrote: > > > Hello, > > I am trying to run a MD simulation on trehalose > (glucose disaccharide) in water. I obtained the PDB file > from the URL: > http://www.rcsb.org/pdb/files/ligand/TRE_model.pdb . When I > run pdb2gmx on the PDB file: > > pdb2gmx -f TRE_model.pdb -o TRE_model.gro -v > > I chose force field 5 (OPLS) from the list: > > Select the Force Field: > 0: GROMOS96 43a1 force field > 1: GROMOS96 43a2 force field (improved alkane > dihedrals) > 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) > 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) > 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) > 5: OPLS-AA/L all-atom force field (2001 > aminoacid dihedrals) > 6: [DEPRECATED] Gromacs force field (see manual) > 7: [DEPRECATED] Gromacs force field with > hydrogens for NMR > 8: Encad all-atom force field, using > scaled-down vacuum charges > 9: Encad all-atom force field, using full > solvent charges > > And I received the following error message: > > ------------------------------------------------------- > Program pdb2gmx, VERSION 4.0.5 > Source code file: pdb2gmx.c, line: 429 > > Fatal error: > Atom C1 in residue TRP 1 not found in rtp entry > with 24 atoms > while sorting atoms > ------------------------------------------------------- > > > > > Well, pdb2gmx thinks that TRE is tryptophan, so it's > looking to complete a TRP building block. Furthermore, your > procedure is undoubtedly going to fail. Force fields and > pdb2gmx are not magic; they are not equipped to handle any > arbitrary molecule you may want to simulate. None of the > force fields provided with Gromacs will contain information > for trehalose by default. There is information for glucose > in some of the force fields (check the .rtp files), and you > may be able to piece trehalose together from that information. > > Otherwise, you will have to go through the *very > difficult and time-consuming* process of parameterization: > > http://oldwiki.gromacs.org/index.php/Parameterization > > -Justin > > > > Please help. > > > Thank you, > > Nancy > > > > > > > > > > -------------------------------------------------------------- > ---------- > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/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/mailing_lists/users.php > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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 gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/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/mailing_lists/users.php > > > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. 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