[gmx-users] SO4

[Justin A. Lemkul]

simon sham wrote:
> Hi,
> I posted this question about SO42- in GROMACS two months ago, but I 
> would like to double-check to confirm my MD results:
> 1. I used gromos53a6.ff force forced for SO42- ion. I have 4 "SO4" ions 
> in the original pdb file.
> 2. When I changed the name "SO4" to "SO42-" in the pdb file as shown in 
> the following line,
> HETATM 1005  S   SO42- A 401      23.925  -3.428   6.383  1.00 
> 35.88           S
> HETATM 1006  O1  SO42- A 401      24.709  -4.359   7.275  1.00 
> 37.19           OM
> HETATM 1007  O2  SO42- A 401      23.433  -4.282   5.270  1.00 
> 37.40           OM
> HETATM 1008  O3  SO42- A 401      22.736  -2.914   7.160  1.00 
> 36.74           OM
> HETATM 1009  O4  SO42- A 401      24.780  -2.306   5.947  1.00 
> 37.08           OM
> HETATM 1010  S   SO42- A 402      22.214  15.738   8.260  1.00 
> 39.60           S
> HETATM 1011  O1  SO42- A 402      21.149  15.021   9.051  1.00 
> 39.06           OM
> HETATM 1012  O2  SO42- A 402      23.462  14.907   7.944  1.00 
> 38.26           OM
> HETATM 1013  O3  SO42- A 402      21.685  16.282   6.925  1.00 
> 39.20           OM
> HETATM 1014  O4  SO42- A 402      22.706  16.910   9.124  1.00 
> 39.69           OM
> HETATM 1015  S   SO42- A 403      34.187   9.439  32.376  1.00 
> 60.41           S
> HETATM 1016  O1  SO42- A 403      35.007   9.343  31.107  1.00 
> 60.53           OM
> HETATM 1017  O2  SO42- A 403      34.378   8.317  33.355  1.00 
> 60.26           OM
> HETATM 1018  O3  SO42- A 403      34.624  10.704  33.093  1.00 
> 60.93           OM
> HETATM 1019  O4  SO42- A 403      32.736   9.578  31.991  1.00 
> 60.64           OM
> and ran "pdb2gmx", instead of having 4 SO42- ions, I only got 1 SO42- 
> ion in the .gro file as follows:
>     0SO42     S 1235   2.390   2.500   2.800
>     0SO42    O1 1236   2.470   0.900   5.900
>     0SO42    O2 1237   2.340   3.300   8.200
>     0SO42    O3 1238   2.270   3.600   1.400
>     0SO42    O4 1239   2.470   8.000   0.600
> And these coordinates are wrong!!
> 
> 3. However, when I used "SO42" in the pdb file, and ran pdb2gmx, I got 
> all the 4 SO42 coordinates, and they are good, but the program gave the 
> following warnings for the SO42 topology:
>  
> WARNING: 'SO42' not found in residue topology database, trying to use 
> 'SO42-'
> 

The coordinate issues and the warning above all derive from the fact that you've 
broken the .pdb file format.  Spacing and lengths of the fields are fixed, and 
by adding two characters to the residue name (which is supposed to be 3 
characters, but 4 are tolerated if the other columns are not shifted), the name 
and coordinates are not read correctly.

Serendipitously, you'll probably get the right parameters anyway, since you want 
SO42-.

Generally, pdb2gmx should not be used for non-repeating molecules.  It is 
designed for proteins and nucleic acids, and to some extent, polymers.  If you 
have SO4 parameters, just write an .itp file and #include it in the system topology.

-Justin

> FYI, I use 4.5.1 version. Did I do something wrong in the pdb file? Can 
> I ignore the warning message in #3?
> 
> Thanks for you help in advance,
> 
> Simon Sham
> 
> 
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================