[gmx-users] PRODRG crash

[Justin A. Lemkul]

Moeed wrote:
> Dear Justin,
> 
> Actually, I used -d option because you said the atoms in the box must be 
> half a bond length from the edges of box...I thought maybe this can be 
> done by -d...
> 

My point was that you should not be using a combination of -box, -d, and -angles 
simultaneously.  Use either -box or -d, not both, and don't use -angles.

> With PRODRG I am unable to produce coordinate file a chain with less 
> than three C atoms.
> I sketched the molecules:
> C-C ethane
> C=C Ethylene
> but I am getting a message:
> 
> ERRDRG> PRODRG does not deal with mono/di-atomic molecules.
> 
> PRODRG> Program terminated unsuccessfully, sorry!
> 
> 
> 1- Could you please help me with this. (actually I need structure file 
> of ethylene in the future)

So make a 4-carbon repeat unit.  It's easy to draw chains with PRODRG (but there 
is a limitation to the number of atoms).

-Justin

> 
> 2- How can I generate structure file of repeating unit -CH2-CH2- with 
> PRODRG. I tried the followings...and all I am getting is the above 
> message.. :(
> 
>  H H
>  | |
>  C-C                                                             
>  | |
>  H H
> 
>  H H
>  | |
> -C-C-
>  | |
>  H H
> 
> -C-C-
> 
> Moeed
> 

-- 
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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

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