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-'
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
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