[gmx-users] Replicating monomer units

[Justin A. Lemkul]

Moeed wrote:
> Hello Justin,
> 
> I spent a full day to find a proper value for -d but it seems there is 
> no way of getting  correct bond lenght and angle at the same time. With 
> the following commands I am getting correct bond length for the atoms 
> connecting two monomer units but the angle is 140. I get 110 angle only 
> when bond distance is much less than actual value (1.53 A). I have also 
> tried monomer units with 6, 8, 10 carbon atoms. For 8 and 10 cases I can 
> not even align carbons with the axis using princ. This proper geometry 
> problem seems to be a very simple thing to figure out but I have reached 
> no results. I would like you to provide me with a hint or suggestion...I 
> appreciate your help. Thanks.
> 

There are two approaches.

1. Use a semi-correct geometry and run energy minimization to resolve any weird 
bonds/angles.

2. Orient your 4-carbon unit properly :)  This requires special index groups for 
the structure you've generated.  The 4-carbon unit is not changed when using 
editconf -princ.  If you use this index file:

[ special ]
   1  3
[ all ]
   1  2  3  4

Run:

editconf -f C4.gro -o C4_princ.gro -n index.ndx -princ

(Choose group 1 for determining the size, 0 for the orientation, and 1 for output)

Then your structure is actually aligned perfectly with the x-axis.  Using 
genconf should be simple at that point.  A little bit of trigonometry will help 
you figure out the proper value of -d.  If you still can't get that to work out, 
then approach #1 may work fine.

-Justin

> Great Red Owns Many ACres of Sand
>     4
>     1Eth     C1    1   0.462   0.285   0.269
>     1Eth     C2    2   0.325   0.216   0.269
>     1Eth     C3    3   0.213   0.321   0.269
>     1Eth     C4    4   0.075   0.255   0.269
>    0.53817   0.53817   0.53817
> 
> editconf -f 4C.pdb -o 4Cd-princ.gro -princ -d 0.075 -bt cubic
> genconf -f 4Cd-princ.gro -o 4Cd-rep.gro -nbox 5 1 1
> 
> 4Cd-rep.gro: replicated units:
> 
> Great Red Owns Many ACres of Sand
>    20
>     1Eth     C1    1   0.462   0.285   0.269  0.0000  0.0000  0.0000
>     1Eth     C2    2   0.325   0.216   0.269  0.0000  0.0000  0.0000
>     1Eth     C3    3   0.213   0.321   0.269  0.0000  0.0000  0.0000
>     1Eth     C4    4   0.075   0.255   0.269  0.0000  0.0000  0.0000
>     2Eth     C1    5   1.000   0.285   0.269  0.0000  0.0000  0.0000
>     2Eth     C2    6   0.863   0.216   0.269  0.0000  0.0000  0.0000
>     2Eth     C3    7   0.751   0.321   0.269  0.0000  0.0000  0.0000
>     2Eth     C4    8   0.613   0.255   0.269  0.0000  0.0000  0.0000
>     3Eth     C1    9   1.538   0.285   0.269  0.0000  0.0000  0.0000
>     3Eth     C2   10   1.401   0.216   0.269  0.0000  0.0000  0.0000
>     3Eth     C3   11   1.289   0.321   0.269  0.0000  0.0000  0.0000
>     3Eth     C4   12   1.151   0.255   0.269  0.0000  0.0000  0.0000
>     4Eth     C1   13   2.077   0.285   0.269  0.0000  0.0000  0.0000
>     4Eth     C2   14   1.940   0.216   0.269  0.0000  0.0000  0.0000
>     4Eth     C3   15   1.828   0.321   0.269  0.0000  0.0000  0.0000
>     4Eth     C4   16   1.690   0.255   0.269  0.0000  0.0000  0.0000
>     5Eth     C1   17   2.615   0.285   0.269  0.0000  0.0000  0.0000
>     5Eth     C2   18   2.478   0.216   0.269  0.0000  0.0000  0.0000
>     5Eth     C3   19   2.366   0.321   0.269  0.0000  0.0000  0.0000
>     5Eth     C4   20   2.228   0.255   0.269  0.0000  0.0000  0.0000
>    2.69085   0.53817   0.53817
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================