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 1 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 10.000 12.0350
[ position restraints ]
1 1 1000 1000 1000 ; restrain every carbon atom to a point
[ molecules ]
carbon 1
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.
-Justin
Cheers,
Ali
--
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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