[gmx-users] Fatal Equilibration Errors

[Bruce D. Ray]

On Sunday, August 9, 2009 at 4:32:19 PM, Nancy <nancy5villa at gmail.com> wrote:

> I obtained the ethylene glycol (1,2-ethanediol) structure from the URL:
>  http://www.rcsb.org/pdb/files/ligand/EDO_ideal.pdb
> 
> I converted the EDO_ideal.pdb file into ethanediol.mol2 using UCSF
> Chimera (http://www.cgl.ucsf.edu/chimera/).
> 
> I then use topolbuild 1.2 (written by Dr. Bruce D. Ray) to generate the topologies:
> 
> $ .../topolbuild1_2_2/src/topolbuild -n ethanediol -dir .../topolbuild1_2_2/dat/gromacs -ff gmx53a6
> 
> which outputs the files:
> 
> ethanediol.gro
> ethanediol.log
> ethanediolMOL.mol2
> ethanediol.top
> ffethanediol.itp
> posreethanediol.itp
> 
> I modified the "ffethanediol.itp" file to read:
> 
> =======================================
> #define _FF_GROMOS96
> #define _FF_GROMOS53A6
> #define _FF_USER
> 
> [ defaults ]
> ;nbfunc     comb-rule      gen-pairs     fudgeLJ      fudgeQQ
>       1             1             no         1.0          1.0
> 
> #include "ffG53a6nb.itp"
> =======================================
> 
> The
lack of hydrogen bonds between the solute and solvent molecules was
> due
to the lack of charges in the generated topology file
"ethanediol.top". 
> So I changed the "atoms" section of the topology
file (the original topology
> file is at the end of this message), and
this causes hydrogen bonds between the
> solute and solvent in numbers
comparable to that between the solvent molecules.
> 
> =======================================
>  [ atoms ]
> ;  nr    type   resnr   residu   atom   cgnr    charge      mass
>     1       CH2     1       EDO      C1    1   0.17600  14.02700       ;   0.0000000
>     2        OA     1       EDO      O1    1   -0.5740  15.99940       ;   0.0000000
>     3        H      1       EDO     HO1    1   0.39800   1.00800       ;   0.0000000
>     4       CH2     1       EDO      C2    2   0.17600  14.02700       ;   0.0000000
>     5        OA     1       EDO      O2    2   -0.5740  15.99940       ;   0.0000000
>     6        H      1       EDO     HO2    2   0.39800   1.00800       ;   0.0000000
> ; total molecule charge =   0.0000000
> =======================================
> 
> I
obtained the charge values from the methanol tutoral included with
Gromacs
>  (.../share/gromacs/tutor/methanol/methanol.itp).  I then
enlarge the box and solvate the molecule:

I used a mol2 file that I generated from a sy2 file downloaded from NCI by first
running the file through dos2unix then replacing the 0 in the residue number
column with 1 EDO so that I had both a correct residue number column with a
residue name column.  The NCI data was missing the residue name column.  I then
read the mol2 file that resulted into UCSF Chimera and used it to generate gasteiger
charges for ethylene glycol.  Chimera wrote the following mol2 file as a result:

@<TRIPOS>MOLECULE
EDO
10 9 1 0 0
SMALL
AMBER99


@<TRIPOS>ATOM
      1 O1          0.0000    0.0000    0.0000 O.3       1 EDO        -0.3940
      2 C1         -0.9400   -0.1600   -1.0400 C.3       1 EDO         0.0662
      3 C2         -1.7400    1.1400   -1.1400 C.3       1 EDO         0.0662
      4 O2         -2.5200    1.2800    0.0200 O.3       1 EDO        -0.3940
      5 H1          0.5196   -0.8024    0.0879 H         1 EDO         0.2102
      6 H2         -1.5882   -0.9871   -0.8384 H         1 EDO         0.0588
      7 H3         -0.4343   -0.3499   -1.9636 H         1 EDO         0.0588
      8 H4         -2.3721    1.1133   -2.0029 H         1 EDO         0.0588
      9 H5         -1.0696    1.9696   -1.2252 H         1 EDO         0.0588
     10 H6         -3.0271    2.0935   -0.0316 H         1 EDO         0.2102
@<TRIPOS>BOND
     1    1    5 1
     2    1    2 1
     3    2    7 1
     4    2    6 1
     5    2    3 1
     6    3    9 1
     7    3    8 1
     8    3    4 1
     9    4   10 1
@<TRIPOS>SUBSTRUCTURE
     1 EDO         2 RESIDUE           4 A     EDO     0 ROOT


I processed this with topolbuild 1.3 and generated topologies with gromacs
53a6 and with opls-aa as the force fields.  I am attaching the results to this
as the tarred and gzipped file, ethanediol.tgz   I note that the opls-aa atom
types selected by topolbuld 1.3 have characteristic atom type charges charges
of -0.7 for each oxygen, +0.435 for each of the two hydrogens bound to oxygens,
+0.06 for each of the hydrogens bound to carbon, and +0.145 for each of the
carbons.  The comparison to the gasteiger charges Chimera assigned to these
atoms is interesting.  The opls-aa topology generated also assigns to the
O1-C1-C2-O2 dihedral the diol constants found as a special define in
ffoplsaabon.itp

{snipped}

> The ethylene glycol lacks explicit non-polar hydrogens; is that
normal for this type of system,
> force field (based on GROMOS96 53a6)
and SPC/E water model?

The 53a6 force field is a united atoms model force field and incorporates non-polar
hydrogens in the parameters of the carbons to which they are bound.  If you want
to treat the non-polar hydrogens separately from the carbons to which they are
bound, you will need to use an all atoms force field such as opls-aa for which I
have included the parameters in the attached tarred and gzipped file, ethanediol.tgz

I hope this is useful.


-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273



      
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