[gmx-users] Re: Hai friends (balu)
If the goal is to simply count the secondary structure, pass the dssp output file through grep __ dssp_output.xpm | wc Fill in the dssp code for each secondary structure in the underline separately. Grep would extract all characters that fit that pattern and wc would count it. Hope that helps. Ali -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Simulating a particle surface for interaction
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 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 -- -- 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 listgmx-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
[gmx-users] Simulating a particle surface for interaction with peptides
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. Cheers, Ali -- gmx-users mailing listgmx-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
