[gmx-users] justin-lipid tutorial........
Hi gromac friends I am performing the justin tutorials on lipids http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials I am strugling now on 3rd steps I have following queris regarding to steps ... 1. I increase the van der walls radii of carbon from the 0.15 to 0.375 Is these also increases the vanderwall radii of protein ...?? If it increases the radii of protein , then how to add water in protein core ...??? 2. What is the meaning of continue to adjust the van der waals radius of carbon ??? Please comment in detail... 3. After solvation I given the following command to ion addition grompp -f ions.mdp -c solv.pdb -p topol.top -o ions.tpr I got following reply ... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8# Generated 837 of the 2346 non-bonded parameter combinations --- Program grompp, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/grompp.c, line: 479 Fatal error: No molecules were defined in the system For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Making merry out of nothing, like in refugee camp (Gogol Bordello) Please give me some valuable suggestion Rama David... With Best Wishes, -- 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] justin-lipid tutorial........
On 5/8/12 8:06 AM, rama david wrote: Hi gromac friends I am performing the justin tutorials on lipids http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials I am strugling now on 3rd steps I have following queris regarding to steps ... 1. I increase the van der walls radii of carbon from the 0.15 to 0.375 Is these also increases the vanderwall radii of protein ...?? If it increases the radii of protein , then how to add water in protein core ...??? It will affect all carbon atoms. If you need to do something more specialized, you'll probably have to use a different approach. The above suggestion is to eliminate water from being placed within the lipid membrane. 2. What is the meaning of continue to adjust the van der waals radius of carbon ??? Please comment in detail... Continue to adjust = change the value until you get satisfactory results. The value of 0.375 generally works well for me, but some lipids pack differently and thus you may need to use a different value. For the tutorial, which uses DPPC, 0.375 should work fine. 3. After solvation I given the following command to ion addition grompp -f ions.mdp -c solv.pdb -p topol.top -o ions.tpr I got following reply ... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8# Generated 837 of the 2346 non-bonded parameter combinations --- Program grompp, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/grompp.c, line: 479 Fatal error: No molecules were defined in the system For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Making merry out of nothing, like in refugee camp (Gogol Bordello) Somehow you've badly broken the topology. At this point, it's hard to say how. -Justin -- 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 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
[gmx-users] Justin-lipid tutorial...
Hi Gromacs friends, I completed the justin lipid tutorials upto the three steps ... While performing the tutorial of lipid written by justin , I get following query.. 1. As per the tutorials we added the DPPC chain topology *; Include DPPC chain topology #include dppc.itp * dppc.itp file has following statement at the last .. #ifdef POSRES_LIPID #include lipid_posre.itp #endif where are these file located If these file are not present why we are not get the any error With best wishes, Rama David -- 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
[gmx-users] Justin-lipid tutorial..
Hi Gromacs Friends, I am doing the justin-lipid tutorial..Link to the tutorial is ... http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html I made the g96_53a6_lipid force field as per the instruction of tutorial.. I have some queris regarding to these new force field 1. As we added the lipid parameter to the force field and so I thought to use these force field to dppc to make topology instead of downloading the topol_dppc.top given by justin. So my command line was pdb2gmx -f dppc128.gro -p kkk.top -o kkk.gro -i kkk.itp -ignh I got the reply Fatal error: Something is wrong in the coordinate formatting of file dppc128.gro. Note that gro is fixed format (see the manual) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I check the gro format .It is right as per my knowledge .. What is the reason for such error??? And can I used that force field to generate the dppc topology instaed of downloading it from tutorial link.. (As we made the changes in force field to adjust with lipid ) Rama david -- 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] Justin-lipid tutorial...
On 5/5/12 2:50 AM, rama david wrote: Hi Gromacs friends, I completed the justin lipid tutorials upto the three steps ... While performing the tutorial of lipid written by justin , I get following query.. 1. As per the tutorials we added the DPPC chain topology *; Include DPPC chain topology #include dppc.itp * dppc.itp file has following statement at the last .. #ifdef POSRES_LIPID #include lipid_posre.itp #endif where are these file located If these file are not present why we are not get the any error Lipid position restraints are only invoked in special cases and are not used in the workflow of the tutorial. The use of lipid_posre.itp is described in the tutorial, however, at: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/advanced_troubleshooting.html You do not get an error about a missing file because the main tutorial does not have you invoke -DPOSRES_LIPID in any of the .mdp files. -Justin -- 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 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] Justin-lipid tutorial..
On 5/5/12 4:01 AM, rama david wrote: Hi Gromacs Friends, I am doing the justin-lipid tutorial..Link to the tutorial is ... http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html I made the g96_53a6_lipid force field as per the instruction of tutorial.. I have some queris regarding to these new force field 1. As we added the lipid parameter to the force field and so I thought to use these force field to dppc to make topology instead of downloading the topol_dppc.top given by justin. So my command line was pdb2gmx -f dppc128.gro -p kkk.top -o kkk.gro -i kkk.itp -ignh I got the reply Fatal error: Something is wrong in the coordinate formatting of file dppc128.gro. Note that gro is fixed format (see the manual) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I check the gro format .It is right as per my knowledge .. What is the reason for such error??? Your impression of the correctness of your .gro file is mistaken. Something is wrong, otherwise pdb2gmx would not complain. There is also no need to run pdb2gmx on a pure DPPC membrane; a simple topology is provided in the tutorial for pure lipids. And can I used that force field to generate the dppc topology instaed of downloading it from tutorial link.. (As we made the changes in force field to adjust with lipid ) If you changed any of the .rtp settings, then you need to use pdb2gmx. If you made changes to dppc.itp, then pdb2gmx will do nothing to help you and you should use the approach mentioned above to obtain your topology. -Justin -- 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 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
