Hi,<br> I want to analysis of the deuterium order parameter of my system containing<br>dppc20-sm20-cholesterol20-<div id="1et3" class="ArwC7c ckChnd">water200tolerance3-bilayer50x50x54.pdb<br>
0 System : 3180 atoms<br>
1 DPPC : 1000 atoms tail 14 to 31 and 32 to 50<br>
2 SM : 1000 atoms tail 14 to 32 and 33 to 50<br>
3 CHOL : 580 atoms tail 22 to 29<br>
4 SOL : 600 atoms<br> Now, I have able to determine the order parameter of only DPPC 128+ water 4000. <br>For this I have followed as instructed in previous mail i.e.<br>making of index file by<br>
make_ndx -f name.pdb<br>del 0-2<br>a C14<br>a C15<br>..<br>and so on.<br>Then,<br></div>g_order -f name.trr -n index.ndx -s topol.tpr -od<br><br>But, I have stuck when I my system contains DPPC, SM, CHOL and water (SOL). The problem is coming from the different numbering of different molecule( i.e. DPPC, SM, CHOL). As I see that for CHOL, there is only one tail starting from 22 to 29 whereas for DPPC, there are two tails starting from 14 to 31 & 32 to 50. Therefore, it gives the following error:<br>
<br>Fatal error:<br>grp 1 does not have same number of elements as grp 1<br><br>I saw that the index file different number of atoms in each group as follows:<br>[ O14 ]<br> 14 64 114 164 214 264 314 364 414 464 514 564 614 664 714 <br>
764 814 864 914 964 <br>[ C15 ]<br> 15 65 115 165 215 265 315 365 415 465 515 565 615 665 715 <br> 765 815 865 915 965 2015 2044 2073 2102 2131 2160 2189 2218 2247 2276 <br>2305 2334 2363 2392 2421 2450 2479 2508 2537 2566 <br>
Again, I think that during the making of index file, I have overlap the counting of tails between DPPC and CHOL.<br><br>How can I overcome my problem and how to make indexfile for a system containg different types of molecules. <br>
Can answer my question clearly with mentioning the commands?<br>Sincerely,<br>Anirban<br><br>