<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><pre><font size="4"><span style="font-family: arial,helvetica,sans-serif;">Hi ALL,</span><br style="font-family: arial,helvetica,sans-serif;"><span style="font-family: arial,helvetica,sans-serif;">I want to do a MD simulation of a GPCR protein using GROMACS vacuum force field. I want to use the old force field G43b1 (vacuum simulation)</span> <br>which is not there in GROMACS4.0.3. I would like to know which is the <span style="font-weight: bold;">substitute for this G43b1</span> force field<br>from the present menu:<br><br>Select the Force Field:<br> 0: GROMOS96 43a1 force field <br> 1: GROMOS96 43a2 force field (improved alkane dihedrals)<br> 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)<br> 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) <br> 4: GROMOS96 53a6 force field (JCC
2004 vol 25 pag 1656) <br> 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<br> 6: [DEPRECATED] Gromacs force field (see manual)<br> 7: [DEPRECATED] Gromacs force field with hydrogens for NMR<br> 8: Encad all-atom force field, using scaled-down vacuum charges<br> 9: Encad all-atom force field, using full solvent charges<br><br>Should I use the 8th one? The new manual for GROMACS4.0 also does not reflect this change.<br>Any suggestion is welcome.<br><br><br>Regards,</font><i><i><font size="4"><br> </font><br></i></i></pre><div> </div><div><font color="#0000bf" size="4"></font> </div><div style="color: rgb(0, 0, 191);"><strong>Anirban Ghosh</strong></div><div style="color: rgb(0, 0, 191);"><strong>Grade Based Engineer<br>Bioinformatics Team<br>Centre for Development of Advanced Computing (C-DAC)<br>Pune, India<br></strong></div><div><br></div></div><br>
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