[gmx-users] Simulating a particle surface for interaction with peptides

[Muhammad Naqvi]

Hi all,
Wonderful community here! FAQs andManuals on one side, nothing beats the advice of experts. Whoever started this forum, thank you. I am learning a lot.

I have a question of my own. I am trying to see the interaction of certain surfactants and co-surfactants at a hydrophobic interface. To that end I have made a gro and top file using the element carbon, minimizing its box size to approximately its atomic radius 0.1nm by editconf, concatenating it by genconf 100 times in x and y directions but only once in z, giving 10000 carbon atoms. This generates a very nice surface. Then I follow up with editconf again to increase the size of the configuration file in the z direction to 10nm as well. So the end result is a 10x10x10nm box with a hydrophobic carbon wall on one side of the box. The wall's integrity is maintained using position restraints of a point for each carbon. To check the correctness of this procedure, I performed a minimization, however, during preprocessing using grompp a fatal error occurred:
 
Last line read:
'[ molecules ]'
Invalid order for directive molecules

I would like to inquire as to what this error is and how to avoid it. Just to verify if the manually produced topology or the configuration files were correct, I processed a benzene ring through the same procedure, ending up with the same error. Here is the topology file:


#include "ffgmx.itp"

[ moleculetype ]
; Name nrexcl
carbon      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       C     1  carbon     CAN     1    0.000  12.0350

[ position restraints ]
1 1 1000 1000 1000 ; restrain every carbon atom to a point

[ molecules ]
carbon 10000

Any help would be highly appreciated. 

Cheers,
Ali