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<span class="Apple-style-span" style="font-family: Tahoma, Verdana, Arial, sans-serif; color: rgb(68, 68, 68); "><pre style="white-space: normal; ">Dear Friends</pre><pre style="white-space: normal; "><br></pre><pre style="white-space: normal; "><span class="Apple-style-span" style="font-family: Tahoma, Verdana, Arial, sans-serif; "><pre style="text-indent: 0in !important; white-space: normal; "> When I applied the g_densmap to my system, my molecule appear in the corner of the xpm file<br style="text-indent: 0in !important; "> and white diffuse regions (maybe by the box rotations) appear.</pre></span></pre><pre style="white-space: normal; ">I used this sequence to obtain the gro file (gro reference used for rotate the box to coincide with the XY molecular plane. The molecule was previously centered).<br><br></pre><pre style="white-space: normal; ">(to make the XY molecular plane coincide with the XY of the box, the group 9 lies on the XY molecular plane)<br> editconf_d -f tmp_prueba.gro -n index.ndx -o tmp_prueba1.gro -princ<br><br><br> Select a group for determining the system size:<br><br> Group 0 ( System) has 6370 elements<br> Group 1 ( HEME) has 47 elements<br> Group 2 ( SOL) has 6321 elements<br> Group 3 ( NA+) has 2 elements<br> Group 4 ( NA) has 1 elements<br> Group 5 ( NC) has 1 elements<br> Group 6 ( CHB) has 1 elements<br> Group 7 ( CHD) has 1 elements<br> Group 8 ( CHB-CHD) has 2 elements<br> Group 9 ( Carb_ring) has 4 elements<br> Group 10 ( CHC) has 1 elements<br> Group 11 ( CHA) has 1 elements<br> Group 12 ( nitrog) has 3 elements<br> Group 13 ( ow_teste) has 1 elements<br> Group 14 ( HW1_HW2) has 4214 elements<br>Group 15 ( OW) has 2107 elements<br> Group 16 ( Fe) has 1 elements<br><br> Select a group: 0<br> Selected 0: 'System'<br><br> system size : 5.486 5.648 6.394 (nm)<br> center : 3.463 3.499 1.671 (nm)<br> box vectors : 4.471 4.471 4.563 (nm)<br> box angles : 60.66 60.66 90.00 (degrees)<br> box volume : 65.78 (nm^3)<br><br> Select group for the determining the orientation<br><br> Group 0 ( System) has 6370 elements<br> Group 1 ( HEME) has 47 elements<br> Group 2 ( SOL) has 6321 elements<br> Group 3 ( NA+) has 2 elements<br> Group 4 ( NA) has 1 elements<br> Group 5 ( NC) has 1 elements<br> Group 6 ( CHB) has 1 elements<br> Group 7 ( CHD) has 1 elements<br> Group 8 ( CHB-CHD) has 2 elements<br> Group 9 ( Carb_ring) has 4 elements<br> Group 10 ( CHC) has 1 elements<br> Group 11 ( CHA) has 1 elements<br> Group 12 ( nitrog) has 3 elements<br> Group 13 ( ow_teste) has 1 elements<br> Group 14 ( HW1_HW2) has 4214 elements<br> Group 15 ( OW) has 2107 elements<br> Group 16 ( Fe) has 1 elements<br><br> Select a group: 9<br> Selected 9: 'Carb_ring '<br><br> new system size : 5.486 5.648 6.394<br> shift : -0.110 -0.145 -0.026 (nm)<br> new center : 3.353 3.353 1.645 (nm)<br> new box vectors : 4.471 4.471 4.563 (nm)<br> new box angles : 60.66 60.66 90.00 (degrees)<br> new box volume : 65.78 (nm^3)<br><br> Select a group for output:<br><br> Group 0 ( System) has 6370 elements<br> Group 1 ( HEME) has 47 elements<br> Group 2 ( SOL) has 6321 elements<br> Group 3 ( NA+) has 2 elements<br> Group 4 ( NA) has 1 elements<br> Group 5 ( NC) has 1 elements<br> Group 6 ( CHB) has 1 elements<br> Group 7 ( CHD) has 1 elements<br> Group 8 ( CHB-CHD) has 2 elements<br> Group 9 ( Carb_ring) has 4 elements<br> Group 10 ( CHC) has 1 elements<br> Group 11 ( CHA) has 1 elements<br> Group 12 ( nitrog) has 3 elements<br> Group 13 ( ow_teste) has 1 elements<br> Group 14 ( HW1_HW2) has 4214 elements<br> Group 15 ( OW) has 2107 elements<br> Group 16 ( Fe) has 1 elements<br><br><br> Select a group: 0<br> Selected 0: 'System'<br><br> * My molecule is well centered and the box axis coincide with the<br> molecular axis (chosen according to my interest)<br><br><br> *The molecule was centered in every step simulation.<br><br><br> trjconv_mpi_d -s heme_centered.tpr -f dm10nsheme.xtc -o<br> dm10nsheme_cent.xtc -center -boxcenter rect -pbc mol<br><br><br> *In every simulation step the box was rotate to XY plane to concide with the XY molecular plane in<br> every step simulation, in this step i used the previously tmp_prueba1.gro)<br><br> trjconv_mpi_d -s tmp_prueba1.gro -f dm10nsheme_cent.xtc -o<br> dm10nsppix_cent_norotTrans.xtc -fit rot+trans<br><br><br> *To obtain the XY density map<br><br> g_densmap_mpi_d -f m10nsppix_cent_norotTrans.xtc -s tmp_prueba1.gro -n<br> index.ndx -o tmpdensmaphemeXY.xpm<br><br><br><br><br><br> Regards<br><br> Ricardo Cuya<br> PUC-Rio, Brasil</pre></span> <br /><hr />Gagnez 10 000 $ avec Hotmail! <a href='http://go.microsoft.com/?linkid=9729713' target='_new'>Participez ici</a></body>
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