Re: Re: [gmx-users] charge assignment for the anomeric carbon in 53a6 ff
Hi Justin, Thanks a lot for the replies. I wonder what are the newer versions you indicated, but I find one as: *A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers*. This new version 56ACARBO is claimed to be nearly equivalent to 53A6 for non-carbohydrate systems, and I find, at least, atomic charges for C1 and C5 look more chemically reasonable. But changes for a couple of 1-4 van der Waals parameter C12 were made to 53a6 force field, and additional atom types were added. So could you tell me which file contain those LJ parameters with respect to different atom types? Alternatively, would it be reasonably good enough to use your Lysozyme-JZ4 strategy, i.e., to build initial topology of carbohydrate molecules by PRODRG, and then modify the atomic charges according to the 56ACARBO paper? Thanks, Yun Shi Yun Shi wrote: Hi all, I am doing MD simulation of some carbohydrate-protein complex with this 53a6 force-field. I noted that in any oligosaccharide, the charge assigned for anomeric carbon is 0.232 while C5 (i.e. in a non-terminal mannopyranose) is 0.376. This is kind of counter-intuitive for me since the anomeric carbon C1 is linked to two oxygen atoms O5 and O1 while C5 is linked to only one oxygen atom O5, and both C1 and C5 are CH type atom. And in other force filed like GLYCAM06, C1 always has a larger positive partial charge than C5. I understand that GROMOS force fields are derived in quite different ways, but I still wonder if it makes sense to switch the charges on C1 and C5? No, but the charges used may not be the best ones anyway. There are newer revisions of 53A6 that are much better. It seems these carbohydrate parameters did not change in the new 54a7 ff, which was tested against nOe and J-coupling data rather than free enthalpy of hydration and solvation, which really puzzles me. 54A7 was principally a revision of protein atom types and one lipid type; nothing in the sugar parameters was modified. -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] charge assignment for the anomeric carbon in 53a6 ff
Yun Shi wrote: Hi Justin, Thanks a lot for the replies. I wonder what are the newer versions you indicated, but I find one as: /A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers/ . This new version 56A_CARBO is claimed to be nearly equivalent to 53A6 for non-carbohydrate systems, and I find, at least, atomic charges for C1 and C5 look more chemically reasonable. But changes for a couple of 1-4 van der Waals parameter C12 were made to 53a6 force field, and additional atom types were added. So could you tell me which file contain those LJ parameters with respect to different atom types? New atom types need to be added to atomtypes.atp and their parameters defined in ffnonbonded.itp. Alternatively, would it be reasonably good enough to use your Lysozyme-JZ4 strategy, i.e., to build initial topology of carbohydrate molecules by PRODRG, and then modify the atomic charges according to the 56A_CARBO paper? Maybe, but check the bonded parameters carefully. Sugars are particularly sensitive to incorrect angle and dihedral parameters, especially. -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] charge assignment for the anomeric carbon in 53a6 ff
Thanks again. Since I am running MD simulation on a public cluster, I cannot modify atomtypes.atp and ffnonbonded.itp on that cluster. But I could get every parameter ready and prepare the xxx.tpr files locally, and pass them to the cluster. So the practical question is, does the tpr file contain all those C12 and C6 LJ parameters already? Or mdrun need to retrieve these parameters according to the atom types from corresponding files within the gromos53a6.ff folder? Regards, Yun Shi Yun Shi wrote: Hi Justin, Thanks a lot for the replies. I wonder what are the newer versions you indicated, but I find one as: /A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers/ . This new version 56A_CARBO is claimed to be nearly equivalent to 53A6 for non-carbohydrate systems, and I find, at least, atomic charges for C1 and C5 look more chemically reasonable. But changes for a couple of 1-4 van der Waals parameter C12 were made to 53a6 force field, and additional atom types were added. So could you tell me which file contain those LJ parameters with respect to different atom types? New atom types need to be added to atomtypes.atp and their parameters defined in ffnonbonded.itp. Alternatively, would it be reasonably good enough to use your Lysozyme-JZ4 strategy, i.e., to build initial topology of carbohydrate molecules by PRODRG, and then modify the atomic charges according to the 56A_CARBO paper? Maybe, but check the bonded parameters carefully. Sugars are particularly sensitive to incorrect angle and dihedral parameters, especially. -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] charge assignment for the anomeric carbon in 53a6 ff
Yun Shi wrote: Thanks again. Since I am running MD simulation on a public cluster, I cannot modify atomtypes.atp and ffnonbonded.itp on that cluster. You can make local copies in your working directory and call that force field when running grompp. But I could get every parameter ready and prepare the xxx.tpr files locally, and pass them to the cluster. So the practical question is, does the tpr file contain all those C12 and C6 LJ parameters already? Or mdrun need to retrieve these parameters according to the atom types from corresponding files within the gromos53a6.ff folder? All the necessary information is contained in the .tpr file. -Justin Regards, Yun Shi Yun Shi wrote: Hi Justin, Thanks a lot for the replies. I wonder what are the newer versions you indicated, but I find one as: /A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers/ . This new version 56A_CARBO is claimed to be nearly equivalent to 53A6 for non-carbohydrate systems, and I find, at least, atomic charges for C1 and C5 look more chemically reasonable. But changes for a couple of 1-4 van der Waals parameter C12 were made to 53a6 force field, and additional atom types were added. So could you tell me which file contain those LJ parameters with respect to different atom types? New atom types need to be added to atomtypes.atp and their parameters defined in ffnonbonded.itp. Alternatively, would it be reasonably good enough to use your Lysozyme-JZ4 strategy, i.e., to build initial topology of carbohydrate molecules by PRODRG, and then modify the atomic charges according to the 56A_CARBO paper? Maybe, but check the bonded parameters carefully. Sugars are particularly sensitive to incorrect angle and dihedral parameters, especially. -Justin -- == == Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/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] charge assignment for the anomeric carbon in 53a6 ff
Yun Shi wrote: Hi all, I am doing MD simulation of some carbohydrate-protein complex with this 53a6 force-field. I noted that in any oligosaccharide, the charge assigned for anomeric carbon is 0.232 while C5 (i.e. in a non-terminal mannopyranose) is 0.376. This is kind of counter-intuitive for me since the anomeric carbon C1 is linked to two oxygen atoms O5 and O1 while C5 is linked to only one oxygen atom O5, and both C1 and C5 are CH type atom. And in other force filed like GLYCAM06, C1 always has a larger positive partial charge than C5. I understand that GROMOS force fields are derived in quite different ways, but I still wonder if it makes sense to switch the charges on C1 and C5? No, but the charges used may not be the best ones anyway. There are newer revisions of 53A6 that are much better. It seems these carbohydrate parameters did not change in the new 54a7 ff, which was tested against nOe and J-coupling data rather than free enthalpy of hydration and solvation, which really puzzles me. 54A7 was principally a revision of protein atom types and one lipid type; nothing in the sugar parameters was modified. -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
