Re: [gmx-users] how to write the correct top file for membrane protein system?
Dear Justin, Thanks for you quickly reply. I have tried before to comment out the section of [ defaults ] in the next itp file, but still too many warnings and final crashed. And i think it would not be the best method to solve this problem, because i have to use ffgmx.itp to deal with DPPC. Is there any other method i can try? Don't mix forcefields unless you already have hard evidence that this combination works - and I'm not aware of any. The link Justin provided warns you about that. You need to find a force field that has parameters optimized that suit your system. Mixing anything else is about 99% likely to make an expensive (and poor) random number generator. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to write the correct top file for membrane protein system?
Dear User, i try to perform simulation on membrane protein ( proterin + DPPC ). And i use OPLS for protein, Berger force field for DPPC. But after i construct this system, i cannot obtain tpr file by using grompp. Here is my topol.top : ; protein #include ffoplsaa.itp #include protein-opls.itp ; membrane #include ffgmx.itp #include lipid.itp #include dppc.itp ; Include water topology #include spc.itp [ system ] ; name Membrane in water [ molecules ] ; name number Protein1 DPPC 123 SOL 14189 here is the result: Fatal error: Invalid order for directive defaults, file /home/gmx331/share/gromacs/top/ffgmx.itp, line 4 Could you please give me some suggestion? i appreciate your help. Thanks so much!___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to write the correct top file for membrane protein system?
Quoting liang [EMAIL PROTECTED]: Dear User, i try to perform simulation on membrane protein ( proterin + DPPC ). And i use OPLS for protein, Berger force field for DPPC. But after i construct this system, i cannot obtain tpr file by using grompp. Here is my topol.top : ; protein #include ffoplsaa.itp #include protein-opls.itp ; membrane #include ffgmx.itp #include lipid.itp #include dppc.itp ; Include water topology #include spc.itp [ system ] ; name Membrane in water [ molecules ] ; name number Protein1 DPPC 123 SOL 14189 here is the result: Fatal error: Invalid order for directive defaults, file /home/gmx331/share/gromacs/top/ffgmx.itp, line 4 I suspect it is a result of using two different force fields. The [ defaults ] will be defined in the first force field (in your case, ffoplsaa.itp), but then grompp is finding a second [ defaults ] in ffgmx.itp. See here: http://wiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file -Justin Could you please give me some suggestion? i appreciate your help. Thanks so much! Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to write the correct top file for membrane protein system?
Dear Justin, Thanks for you quickly reply. I have tried before to comment out the section of [ defaults ] in the next itp file, but still too many warnings and final crashed. And i think it would not be the best method to solve this problem, because i have to use ffgmx.itp to deal with DPPC. Is there any other method i can try? Thanks Liang - Original Message - From: Justin A. Lemkul [EMAIL PROTECTED] To: liang [EMAIL PROTECTED]; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, November 25, 2007 12:23 PM Subject: Re: [gmx-users] how to write the correct top file for membrane protein system? Quoting liang [EMAIL PROTECTED]: Dear User, i try to perform simulation on membrane protein ( proterin + DPPC ). And i use OPLS for protein, Berger force field for DPPC. But after i construct this system, i cannot obtain tpr file by using grompp. Here is my topol.top : ; protein #include ffoplsaa.itp #include protein-opls.itp ; membrane #include ffgmx.itp #include lipid.itp #include dppc.itp ; Include water topology #include spc.itp [ system ] ; name Membrane in water [ molecules ] ; name number Protein1 DPPC 123 SOL 14189 here is the result: Fatal error: Invalid order for directive defaults, file /home/gmx331/share/gromacs/top/ffgmx.itp, line 4 I suspect it is a result of using two different force fields. The [ defaults ] will be defined in the first force field (in your case, ffoplsaa.itp), but then grompp is finding a second [ defaults ] in ffgmx.itp. See here: http://wiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file -Justin Could you please give me some suggestion? i appreciate your help. Thanks so much! Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
