High-throughput "in silico" screening (e.g. for ligand-protein binding) has been performed on a number of systems. How are such automated simulations performed (I assume they utilize molecular dynamics)?
On Fri, Jul 31, 2009 at 5:47 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Nancy wrote: > >> 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? >> >> > Indeed it would be nice if there was a software package that would > parameterize your molecule, validate said parameters, then run a meaningful > simulation with all the proper conditions. Maybe it could even make > coffee... > > All kidding aside, the answer is no. It is the job of the user to generate > and validate parameters when none are available. A proper topology is > perhaps the most important part of setting up a simulation! > > There are some methods for doing some of this in an automated fashion > (i.e., RESP charge derivation, antechamber with GAFF, etc). But the hard > truth comes down to one simple fact - if no parameters are already > available, you must do that work. It is hard, but necessary. Have a look > at the Gromos96 force fields; they contain some monosaccharide building > blocks that should give you a reasonable starting point. > > -Justin > > Thanks, >> >> Nancy >> >> >> >> >> >> On Fri, Jul 31, 2009 at 4:53 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> 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 >> <mailto: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 >> <mailto: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 <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto: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. 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 >
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