[gmx-users] Carbohydrate MD Simulation

[Jim Kress]

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-bounces at gromacs.org 
> [mailto:gmx-users-bounces at 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 
> <jalemkul at 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
> 		
> 		
> 		
> 		
> 		
> 		
> 		
> 		
> 		
> --------------------------------------------------------------
> ----------
> 		
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> 
> 	-- 
> 	========================================
> 	
> 	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
> 	
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