<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV><BR><BR>Dear sir :</DIV>
<DIV>I want to a pentamer membrane protein, when I used InflateGRO.pl with <EM>DOUGHNUT Mode, the results were wrong, please help me! </EM><BR><A class=plink href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" rel=nofollow target=_blank><IMG class=pimg border=0 alt=4 src="http://opi.yahoo.com/online?u=zhaoxiitc2002&t=4&l=cn"></A>show " [user@localhost protein-tutorial]$ perl inflategro.txt kkr.gro 4 POPC 14 kk_inflated.gro 5 area.dat doughnut protein_subunits<BR>Doughnut mode activated. Protein coordinates will be translated by subunit ....<BR>Reading..... <BR>Reading chain identifiers.... <BR>Subunit 1: atom 1 to atom 3238 <BR>Subunit 2: atom 3239 to atom 6476 <BR>Subunit 3: atom 6477 to atom 9714 <BR>Subunit 4: atom 9715 to atom 12952 <BR>Subunit 5: atom 12953 to atom 16190 <BR>There are 5 protein
subunits.... <BR>Scaling lipids....<BR>There are 512 lipids...<BR>with 65 atoms per lipid..</DIV>
<DIV>Determining upper and lower leaflet...<BR>256 lipids in the upper...<BR>256 lipids in the lower leaflet </DIV>
<DIV>Checking for overlap....<BR>...this might actually take a while...</DIV>
<DIV>.......</DIV>
<DIV>Argument "N4" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.<BR>Argument "C5" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.<BR>Argument "C6" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.<BR>Argument "O7" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.<BR>Argument "P8" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.<BR>Argument "O9" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.<BR>Argument "A1" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.<BR>Argument "A2" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.<BR>Argument "C1" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.<BR>Argument "C2" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.<BR>Argument "C3" isn't numeric in printf at
inflategro.txt line 708, <CHAINS> line 5.<BR>Argument "N4" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.<BR>Argument "C5" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.<BR>Argument "C6" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.<BR>Argument "O7" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.<BR>Argument "P8" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.<BR>Argument "O9" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.<BR>Argument "A1" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.<BR>Argument "A2" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.</DIV>
<DIV>Calculating Area per lipid...<BR>Protein X-min/max: 23 105<BR>Protein Y-min/max: 18 100<BR>X-range: 82 A Y-range: 82 A<BR>Building 82 X 82 2D grid on protein coordinates...<BR>Calculating area occupied by protein..<BR>full TMD..<BR>upper TMD....<BR>lower TMD....<BR>Area per protein: 49 nm^2<BR>Area per lipid: 9.83158146861789 nm^2</DIV>
<DIV>Area per protein, upper half: 38.75 nm^2<BR>Area per lipid, upper leaflet : 9.79362516645161 nm^2</DIV>
<DIV>Area per protein, lower half: 45.75 nm^2<BR>Area per lipid, lower leaflet : 9.92548787409836 nm^2</DIV>
<DIV>Writing Area per lipid...<BR>Done!</DIV></td></tr></table><br>