[gmx-users] PRODRG crash

Moeed lecielll at googlemail.com
Tue Jun 22 19:05:53 CEST 2010

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...

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)

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
 | |
 | |
 H H

 H H
 | |
 | |
 H H


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