Dear Justin,<br><br>Indeed I didnt take into account square degree so all values presented in the tutorial exactly true so this was exactly my mistake. :( <br><br>After some iterations I've obtained value for S per lipid beetween 0.65-0.71 A^2. This is the example of the system wich I've obtained after solvation and futher minimization. <a href="http://www.sendspace.com/file/h6urhq">http://www.sendspace.com/file/h6urhq</a> It looks good. :) By the way I'd like to know about correct value for the S per protein ? Where I can obtain such information for my protein ? ( e.g for big proteins such receptors and channels )<br>
<br>The error with GenBox was due to the big vdv R for the carbons. It's intresting that I couldnt increase this value mush as 1.2. But my finally system didnt consist of some water within the membrane so I supose that it's good.<br>
<br>Now my system on the stage of the equilibtation so I have not any questions yet but I only wounder to know about teqnique of the force fied preparation for the membrane protein simulation.<br><br>In this work I've done this step in accordance with the tutorial. On the last stage I've copied <font face="Arial"><font size="3"> gromos53a6_lipid.ff directory in $GMXLIB so now I can use it in pdb2gmx for instance. <br>
But when I've tried to make gro and top files for my lipid.pdb via pdb2gmx I've obtained errors that Residue 'DPP' not found in residue topology database so I think that in addition to the operations wich I've already done I should also make some changes in the<br>
/gromos53a6_lipid.ff/aminoacids.hdb<br> ./gromos53a6_lipid.ff/aminoacids.n.tdb<br> ./gromos53a6_lipid.ff/aminoacids.c.tdb<br>shouldn't I?<br><br>Finally, I've heard that there are already pre-build force fields for the membrane smulation. E.g I've heard that there is some modified CHARMM ff wich gave good results in simulation. Do you know something about this?<br>
<br><br>Thank you for your help,<br><br>James <br><br></font></font>