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

Justin A. Lemkul jalemkul at vt.edu
Sun Feb 7 07:55:24 CET 2010

Muhammad Naqvi wrote:
> 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. 

See the manual, Table 5.3 - you're missing the mandatory [system] directive.  If 
you get an "invalid order" error, either something is out of order or missing.


> Cheers,
> Ali


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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