Re: [gmx-users] Topology dihedral or improper dihedral
On Sun, Nov 13, 2011 at 10:26 AM, XUEMING TANG yujan2...@gmail.com wrote: Hi there I am trying to build up a topology file for a tetra nitrogen molecule using Gromos UA and OPLS UA force field. Following are the molecules. 1. for C | A. C-C-C-C-C-C-C-N-C and | C C | B. C-C-C-C-C-C-C-N-C-C-C-C-COOH | C I have several questions: For A, the first molecule, should I use improper dihedral for the N-(CH3)3 or proper dihedral for C-C-N-C with multi 3 for the head group? Is there any differences when using different force field (GROMOS and OPLS-UA)? For B, the second molecule, should I use improper dihedral for the N-(CH3)3 or proer dihedral for C-C-N-C with multi 2? Is there any differences when using different force field (GROMOS UA and OPLS UA)? The first expression about improper didedral is a planer restriction. When read the manual it also refers to the tetrahedral structure like this tetra nitrogen functional group. My question is when it has really long hydrocarbon tail, I guess it will be hard to flip over to the mirror images. Or it is not true in the simulation? You may take one built by other server, such as http://davapc1.bioch.dundee.ac.uk/prodrg/ as reference, and built yourself if necessary. Thank you very much!!! Best! Xueming -- 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/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 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] Topology dihedral or improper dihedral
Thank you for your reply, Lina. I did try the prodrg server before. For A molecule, there is no improper dihedral. A just has one dihedral for the head group. For B molecule, it gives improper dihedral of the tetra nitrogen. I am wondering what is the criteria or at least a guidance of what could be the best choice for the topology file. Or any choices could be right and I have to try which one provide consistent results with experiment by trial? Best! Xueming On Sun, Nov 13, 2011 at 9:57 AM, lina lina.lastn...@gmail.com wrote: On Sun, Nov 13, 2011 at 10:26 AM, XUEMING TANG yujan2...@gmail.com wrote: Hi there I am trying to build up a topology file for a tetra nitrogen molecule using Gromos UA and OPLS UA force field. Following are the molecules. 1. for C | A. C-C-C-C-C-C-C-N-C and | C C | B. C-C-C-C-C-C-C-N-C-C-C-C-COOH | C I have several questions: For A, the first molecule, should I use improper dihedral for the N-(CH3)3 or proper dihedral for C-C-N-C with multi 3 for the head group? Is there any differences when using different force field (GROMOS and OPLS-UA)? For B, the second molecule, should I use improper dihedral for the N-(CH3)3 or proer dihedral for C-C-N-C with multi 2? Is there any differences when using different force field (GROMOS UA and OPLS UA)? The first expression about improper didedral is a planer restriction. When read the manual it also refers to the tetrahedral structure like this tetra nitrogen functional group. My question is when it has really long hydrocarbon tail, I guess it will be hard to flip over to the mirror images. Or it is not true in the simulation? You may take one built by other server, such as http://davapc1.bioch.dundee.ac.uk/prodrg/ as reference, and built yourself if necessary. Thank you very much!!! Best! Xueming -- 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 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 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] Topology dihedral or improper dihedral
XUEMING TANG wrote: Thank you for your reply, Lina. I did try the prodrg server before. For A molecule, there is no improper dihedral. A just has one dihedral for the head group. For B molecule, it gives improper dihedral of the tetra nitrogen. I am wondering what is the criteria or at least a guidance of what could be the best choice for the topology file. Or any choices could be right and I have to try which one provide consistent results with experiment by trial? I see no reason why a quaternary nitrogen would need an improper dihedral assigned to it. Some impropers in Gromos96 are applied to tetrahedral groups like alpha-carbons because there is no explicit H atom present, thus the stereochemistry is maintained with an improper so that the groups do not invert. With four explicit substituents, an improper should not be necessary. -Justin Best! Xueming On Sun, Nov 13, 2011 at 9:57 AM, lina lina.lastn...@gmail.com mailto:lina.lastn...@gmail.com wrote: On Sun, Nov 13, 2011 at 10:26 AM, XUEMING TANG yujan2...@gmail.com mailto:yujan2...@gmail.com wrote: Hi there I am trying to build up a topology file for a tetra nitrogen molecule using Gromos UA and OPLS UA force field. Following are the molecules. 1. for C | A. C-C-C-C-C-C-C-N-C and | C C | B. C-C-C-C-C-C-C-N-C-C-C-C-COOH | C I have several questions: For A, the first molecule, should I use improper dihedral for the N-(CH3)3 or proper dihedral for C-C-N-C with multi 3 for the head group? Is there any differences when using different force field (GROMOS and OPLS-UA)? For B, the second molecule, should I use improper dihedral for the N-(CH3)3 or proer dihedral for C-C-N-C with multi 2? Is there any differences when using different force field (GROMOS UA and OPLS UA)? The first expression about improper didedral is a planer restriction. When read the manual it also refers to the tetrahedral structure like this tetra nitrogen functional group. My question is when it has really long hydrocarbon tail, I guess it will be hard to flip over to the mirror images. Or it is not true in the simulation? You may take one built by other server, such as http://davapc1.bioch.dundee.ac.uk/prodrg/ as reference, and built yourself if necessary. Thank you very much!!! Best! Xueming -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Topology dihedral or improper dihedral
Hi there I am trying to build up a topology file for a tetra nitrogen molecule using Gromos UA and OPLS UA force field. Following are the molecules. 1. for C | A. C-C-C-C-C-C-C-N-C and | C C | B. C-C-C-C-C-C-C-N-C-C-C-C-COOH | C I have several questions: For A, the first molecule, should I use improper dihedral for the N-(CH3)3 or proper dihedral for C-C-N-C with multi 3 for the head group? Is there any differences when using different force field (GROMOS and OPLS-UA)? For B, the second molecule, should I use improper dihedral for the N-(CH3)3 or proer dihedral for C-C-N-C with multi 2? Is there any differences when using different force field (GROMOS UA and OPLS UA)? The first expression about improper didedral is a planer restriction. When read the manual it also refers to the tetrahedral structure like this tetra nitrogen functional group. My question is when it has really long hydrocarbon tail, I guess it will be hard to flip over to the mirror images. Or it is not true in the simulation? Thank you very much!!! Best! Xueming -- 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
