<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hi,<br>I posted this question about SO42- in GROMACS two months ago, but I would like to double-check to confirm my MD results:<br>1. I used gromos53a6.ff force forced for SO42- ion. I have 4 "SO4" ions in the original pdb file.<br>2. When I changed the name "SO4" to "SO42-" in the pdb file as shown in the following line,<br>HETATM 1005 S SO42- A 401 23.925 -3.428 6.383 1.00 35.88 S<br>HETATM 1006 O1 SO42- A 401 24.709 -4.359 7.275 1.00 37.19 OM<br>HETATM 1007 O2 SO42- A 401 23.433 -4.282 5.270 1.00
37.40 OM<br>HETATM 1008 O3 SO42- A 401 22.736 -2.914 7.160 1.00 36.74 OM<br>HETATM 1009 O4 SO42- A 401 24.780 -2.306 5.947 1.00 37.08 OM<br>HETATM 1010 S SO42- A 402 22.214 15.738 8.260 1.00 39.60 S<br>HETATM 1011 O1 SO42- A 402 21.149 15.021 9.051 1.00 39.06 OM<br>HETATM 1012 O2 SO42- A 402 23.462 14.907 7.944 1.00
38.26 OM<br>HETATM 1013 O3 SO42- A 402 21.685 16.282 6.925 1.00 39.20 OM<br>HETATM 1014 O4 SO42- A 402 22.706 16.910 9.124 1.00 39.69 OM<br>HETATM 1015 S SO42- A 403 34.187 9.439 32.376 1.00 60.41 S<br>HETATM 1016 O1 SO42- A 403 35.007 9.343 31.107 1.00 60.53 OM<br>HETATM 1017 O2 SO42- A 403 34.378 8.317 33.355 1.00
60.26 OM<br>HETATM 1018 O3 SO42- A 403 34.624 10.704 33.093 1.00 60.93 OM<br>HETATM 1019 O4 SO42- A 403 32.736 9.578 31.991 1.00 60.64 OM<br>and ran "pdb2gmx", instead of having 4 SO42- ions, I only got 1 SO42- ion in the .gro file as follows:<br> 0SO42 S 1235 2.390 2.500 2.800<br> 0SO42 O1 1236 2.470 0.900 5.900<br> 0SO42 O2 1237 2.340 3.300 8.200<br> 0SO42 O3 1238 2.270
3.600 1.400<br> 0SO42 O4 1239 2.470 8.000 0.600<br>And these coordinates are wrong!!<br><br>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:<br> <br>WARNING: 'SO42' not found in residue topology database, trying to use 'SO42-'<br><br>FYI, I use 4.5.1 version. Did I do something wrong in the pdb file? Can I ignore the warning message in #3?<br><br>Thanks for you help in advance,<br><br>Simon Sham<br><br><br><br></td></tr></table><br>