[gmx-users] deuterim order parameter

[Justin A. Lemkul]

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

Since you likely have the same atom naming in multiple molecules, typing simply 
"a C15" is asking for trouble!

Specify the residue *and* atom name, and you will get things squared away.  The 
help info that make_ndx will print for you should be able to help you.

-Justin

> Sincerely,
> Anirban
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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