Nice! Thank you!
> 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. > > -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 > > ======================================== > > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 70, Issue 41 > ***************************************** -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php