[gmx-users] Carbohydrate MD Simulation

[Justin A. Lemkul]

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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