Re: [gmx-users] parameters for bond types for GROMOS force field.
Justin 1) So if I understood correctly I can make parametrisation of my uncommon group by the atb for instance. Than I can change itp file to rtp form and integrate this new residue to the existing ff. Finally when I will run pdb2gmx on the protein with the same group (even with different atom order) I obtain proper topology.top file. Doest it correct ? 2) I've defined bond between both of my atoms as the gb_15 and define this atoms as the C in the topology.top. Than I've run minimisation and short 3ns MD_run. Unfortunatelly this atoms was in the sp3 form and were not in the planar form :( What else should I do ? Could some operations with the angle term in topology.top help me? I've modified 612 613 614 2 as thega_27 but it also could not help me. James 2012/6/10 Justin A. Lemkul jalem...@vt.edu On 6/10/12 8:03 AM, James Starlight wrote: Justin, thanks again for help. Finally is there any generall solution to parametrise hetero-groups covalently bonded with the protein ? Many proteins consist of such groups e.g chromophore in GFP, retinall in rhodopsin as well as some prostetic groups in the enzymes. Parameterization schemes differ across force fields. It's never easy. I've tried to make something like you've told me via inclusion of pre-parametrised residues in the existing gromacs ff but forced with some problems due to the atom order in new ITP and gro files provided by ATb or PRODRG are different from initial pdb file so pdb2gmx on the whole protein where het-group in the old order would not work properly :( The output .itp files of ATB or PRODRG are not what you should be using. You can't #include a covalently attached residue and expect the resulting dynamics to be relevant; it's not like a ligand. What you need to do in those cases is create an .rtp entry (and any other incidental bonded and nonbonded additions, as stated before) that specifies whatever parameters you believe to be reliable. At that point, when the .rtp file is read, the atom order is irrelevant - if pdb2gmx finds the atoms it needs, it builds the topology. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] parameters for bond types for GROMOS force field.
On 11/06/2012 6:12 PM, James Starlight wrote: Justin 1) So if I understood correctly I can make parametrisation of my uncommon group by the atb for instance. Than I can change itp file to rtp form and integrate this new residue to the existing ff. Finally when I will run pdb2gmx on the protein with the same group (even with different atom order) I obtain proper topology.top file. Doest it correct ? The change to which you refer will be non-trivial because of the covalent bond. Charge distribution and atom types will change. 2) I've defined bond between both of my atoms as the gb_15 and define this atoms as the C in the topology.top. Than I've run minimisation and short 3ns MD_run. Unfortunatelly this atoms was in the sp3 form and were not in the planar form :( What else should I do ? Could some operations with the angle term in topology.top help me? I've modified 612 613 614 2 as thega_27 but it also could not help me. It is possible to hack something that will work, but the transferability of charges from an isolated form to a form covalently bound to a peptide is (at best) doubtful. If your atomic arrangement is changing, the presence of single vs double bonds must be changing, and that should basically guarantee non-transferability. The most correct form of a solution is to parameterise the modified form of the residue along the same lines as the original force field parameterization. That may or may not be feasible for you. It's hard to be more specific without knowing exactly what modified residue you are seeking to create. Mark James 2012/6/10 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu On 6/10/12 8:03 AM, James Starlight wrote: Justin, thanks again for help. Finally is there any generall solution to parametrise hetero-groups covalently bonded with the protein ? Many proteins consist of such groups e.g chromophore in GFP, retinall in rhodopsin as well as some prostetic groups in the enzymes. Parameterization schemes differ across force fields. It's never easy. I've tried to make something like you've told me via inclusion of pre-parametrised residues in the existing gromacs ff but forced with some problems due to the atom order in new ITP and gro files provided by ATb or PRODRG are different from initial pdb file so pdb2gmx on the whole protein where het-group in the old order would not work properly :( The output .itp files of ATB or PRODRG are not what you should be using. You can't #include a covalently attached residue and expect the resulting dynamics to be relevant; it's not like a ligand. What you need to do in those cases is create an .rtp entry (and any other incidental bonded and nonbonded additions, as stated before) that specifies whatever parameters you believe to be reliable. At that point, when the .rtp file is read, the atom order is irrelevant - if pdb2gmx finds the atoms it needs, it builds the topology. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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 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] parameters for bond types for GROMOS force field.
Justin I have one extra question about parametrisation of the bond type Initially I had -c-c- bond so both atoms were in the sp3 hybridization. I've changed bond type between that atoms to the gb_16 ( from phe ring) to define them as the c=c but during the simulation I've noticed that the bond between that atoms is not planar ( sp2 form) and still is in the sp3. What addition changees should I do in my topology to change the planarity of new bond ? Should I make some changes ia angles term as well? E.g I've found 612 613 614 2ga_13 ; where 612 and 613 are the atoms wich I would like to present as the rigid. I've change to the ga_27 ( 120) but during simulation the bond was still in sp3. What I've done wrong ? James 2012/6/8 James Starlight jmsstarli...@gmail.com Justin, thanks alot. I'll try to use gb_10 ( for C=N) as well as gb_16 ( for C=C) for parametrisation in my task. James 2012/6/8 Justin A. Lemkul jalem...@vt.edu On 6/8/12 2:01 PM, James Starlight wrote: Justin, Does the gb_10 suitable for both bonds that I want to parametrise ? As I've told previously I need to parametrise two different bonds 1) is the C=C bond wich are not in the ring. This is just double bound in linnear sequence -C=C-. 2) is the C=N- double bond where both atoms in the 5-m ring system This is a better description. The last message suggested everything was in a 5-membered ring. Had that been the case, my suggestion would have been right (see, for instance, a HIS side chain - gb_10 is used for both C=C and C=N in that case). There are no linear C=C bonds in Gromos force fields by default, as such groups are not in proteins. The closest you can likely come is to take a C=C bond from the PHE ring. Bond lengths are simple, and are usually derived from spectroscopic information. If using constraints on all bonds, the force constant is irrelevant since the bond is rigid. If not using constraints, then you'll have to find or derive suitable parameters yourself. Welcome to the inconvenient world of parameterization :) -Justin Thanks again, James 2012/6/8 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu On 6/8/12 1:22 PM, James Starlight wrote: I've found that information in ffbonded.itp but I'm not sure about exactly meaning of some types. E.g I'm looking for bond type for simple double bond between C=C as well as C=N ( here both atoms in 5-m ring) atoms pairs. Should I use for the first one #define gb_15 0.1390 8.6600e+06 ; CH2 - C, CR1 (6-ring) 800 and for the second one ; #define gb_11 0.1340 1.0500e+07 ; C - N, NZ, NE 900 ? Neither. gb_10 sounds exactly like what you need: #define gb_10 0.1330 1.1800e+07 ; C, CR1 - N, NR, CR1, C (peptide, 5-ring) 1000 -Justin -- ==**__== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing list gmx-users@gromacs.org mailto: gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search
Re: [gmx-users] parameters for bond types for GROMOS force field.
On 6/10/12 3:06 AM, James Starlight wrote: Justin I have one extra question about parametrisation of the bond type Initially I had -c-c- bond so both atoms were in the sp3 hybridization. I've changed bond type between that atoms to the gb_16 ( from phe ring) to define them as the c=c but during the simulation I've noticed that the bond between that atoms is not planar ( sp2 form) and still is in the sp3. What addition changees should I do in my topology to change the planarity of new bond ? Defining appropriate atom types will be necessary here, as well. For a single bond, the atom types would be -CH2-CH2- while a double bond will necessarily be -CH=CH- Also note that with a united atom representation, it's very hard to make such assertions about hybridization state. There are no hydrogens, so the geometry of these central carbons is not easily defined. Should I make some changes ia angles term as well? E.g I've found 612 613 614 2ga_13 ; where 612 and 613 are the atoms wich I would like to present as the rigid. I've change to the ga_27 ( 120) but during simulation the bond was still in sp3. What I've done wrong ? As there are no parameters for linear C=C bonds in the Gromos force fields, you may have to do some parameterization yourself, particularly for appropriate dihedrals. One option is to look at how these bonds are treated in lipid force fields like the Berger parameter set, distributed by Peter Tieleman's group. There are double bonds defined for lipids like POPC. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] parameters for bond types for GROMOS force field.
Justin, thanks again for help. Finally is there any generall solution to parametrise hetero-groups covalently bonded with the protein ? Many proteins consist of such groups e.g chromophore in GFP, retinall in rhodopsin as well as some prostetic groups in the enzymes. I've tried to make something like you've told me via inclusion of pre-parametrised residues in the existing gromacs ff but forced with some problems due to the atom order in new ITP and gro files provided by ATb or PRODRG are different from initial pdb file so pdb2gmx on the whole protein where het-group in the old order would not work properly :( James 2012/6/10 Justin A. Lemkul jalem...@vt.edu On 6/10/12 3:06 AM, James Starlight wrote: Justin I have one extra question about parametrisation of the bond type Initially I had -c-c- bond so both atoms were in the sp3 hybridization. I've changed bond type between that atoms to the gb_16 ( from phe ring) to define them as the c=c but during the simulation I've noticed that the bond between that atoms is not planar ( sp2 form) and still is in the sp3. What addition changees should I do in my topology to change the planarity of new bond ? Defining appropriate atom types will be necessary here, as well. For a single bond, the atom types would be -CH2-CH2- while a double bond will necessarily be -CH=CH- Also note that with a united atom representation, it's very hard to make such assertions about hybridization state. There are no hydrogens, so the geometry of these central carbons is not easily defined. Should I make some changes ia angles term as well? E.g I've found 612 613 614 2ga_13 ; where 612 and 613 are the atoms wich I would like to present as the rigid. I've change to the ga_27 ( 120) but during simulation the bond was still in sp3. What I've done wrong ? As there are no parameters for linear C=C bonds in the Gromos force fields, you may have to do some parameterization yourself, particularly for appropriate dihedrals. One option is to look at how these bonds are treated in lipid force fields like the Berger parameter set, distributed by Peter Tieleman's group. There are double bonds defined for lipids like POPC. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] parameters for bond types for GROMOS force field.
On 6/10/12 8:03 AM, James Starlight wrote: Justin, thanks again for help. Finally is there any generall solution to parametrise hetero-groups covalently bonded with the protein ? Many proteins consist of such groups e.g chromophore in GFP, retinall in rhodopsin as well as some prostetic groups in the enzymes. Parameterization schemes differ across force fields. It's never easy. I've tried to make something like you've told me via inclusion of pre-parametrised residues in the existing gromacs ff but forced with some problems due to the atom order in new ITP and gro files provided by ATb or PRODRG are different from initial pdb file so pdb2gmx on the whole protein where het-group in the old order would not work properly :( The output .itp files of ATB or PRODRG are not what you should be using. You can't #include a covalently attached residue and expect the resulting dynamics to be relevant; it's not like a ligand. What you need to do in those cases is create an .rtp entry (and any other incidental bonded and nonbonded additions, as stated before) that specifies whatever parameters you believe to be reliable. At that point, when the .rtp file is read, the atom order is irrelevant - if pdb2gmx finds the atoms it needs, it builds the topology. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] parameters for bond types for GROMOS force field.
On 9/06/2012 12:00 AM, James Starlight wrote: Dear Gromacs Users! I'm looking for description of the parameters of bonds terms ( termed as the gb_# in the topology.top file) . Could you tell me where I could find such descriptions for all possible bond types ? See manual for literature references for the force field components. Mark -- 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] parameters for bond types for GROMOS force field.
I've found that information in ffbonded.itp but I'm not sure about exactly meaning of some types. E.g I'm looking for bond type for simple double bond between C=C as well as C=N ( here both atoms in 5-m ring) atoms pairs. Should I use for the first one #define gb_15 0.1390 8.6600e+06 ; CH2 - C, CR1 (6-ring) 800 and for the second one ; #define gb_11 0.1340 1.0500e+07 ; C - N, NZ, NE 900 ? Thanks for help James 2012/6/8 Mark Abraham mark.abra...@anu.edu.au On 9/06/2012 12:00 AM, James Starlight wrote: Dear Gromacs Users! I'm looking for description of the parameters of bonds terms ( termed as the gb_# in the topology.top file) . Could you tell me where I could find such descriptions for all possible bond types ? See manual for literature references for the force field components. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] parameters for bond types for GROMOS force field.
On 6/8/12 1:22 PM, James Starlight wrote: I've found that information in ffbonded.itp but I'm not sure about exactly meaning of some types. E.g I'm looking for bond type for simple double bond between C=C as well as C=N ( here both atoms in 5-m ring) atoms pairs. Should I use for the first one #define gb_15 0.1390 8.6600e+06 ; CH2 - C, CR1 (6-ring) 800 and for the second one ; #define gb_11 0.1340 1.0500e+07 ; C - N, NZ, NE 900 ? Neither. gb_10 sounds exactly like what you need: #define gb_10 0.1330 1.1800e+07 ; C, CR1 - N, NR, CR1, C (peptide, 5-ring) 1000 -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] parameters for bond types for GROMOS force field.
Justin, Does the gb_10 suitable for both bonds that I want to parametrise ? As I've told previously I need to parametrise two different bonds 1) is the C=C bond wich are not in the ring. This is just double bound in linnear sequence -C=C-. 2) is the C=N- double bond where both atoms in the 5-m ring system Thanks again, James 2012/6/8 Justin A. Lemkul jalem...@vt.edu On 6/8/12 1:22 PM, James Starlight wrote: I've found that information in ffbonded.itp but I'm not sure about exactly meaning of some types. E.g I'm looking for bond type for simple double bond between C=C as well as C=N ( here both atoms in 5-m ring) atoms pairs. Should I use for the first one #define gb_15 0.1390 8.6600e+06 ; CH2 - C, CR1 (6-ring) 800 and for the second one ; #define gb_11 0.1340 1.0500e+07 ; C - N, NZ, NE 900 ? Neither. gb_10 sounds exactly like what you need: #define gb_10 0.1330 1.1800e+07 ; C, CR1 - N, NR, CR1, C (peptide, 5-ring) 1000 -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] parameters for bond types for GROMOS force field.
On 6/8/12 2:01 PM, James Starlight wrote: Justin, Does the gb_10 suitable for both bonds that I want to parametrise ? As I've told previously I need to parametrise two different bonds 1) is the C=C bond wich are not in the ring. This is just double bound in linnear sequence -C=C-. 2) is the C=N- double bond where both atoms in the 5-m ring system This is a better description. The last message suggested everything was in a 5-membered ring. Had that been the case, my suggestion would have been right (see, for instance, a HIS side chain - gb_10 is used for both C=C and C=N in that case). There are no linear C=C bonds in Gromos force fields by default, as such groups are not in proteins. The closest you can likely come is to take a C=C bond from the PHE ring. Bond lengths are simple, and are usually derived from spectroscopic information. If using constraints on all bonds, the force constant is irrelevant since the bond is rigid. If not using constraints, then you'll have to find or derive suitable parameters yourself. Welcome to the inconvenient world of parameterization :) -Justin Thanks again, James 2012/6/8 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu On 6/8/12 1:22 PM, James Starlight wrote: I've found that information in ffbonded.itp but I'm not sure about exactly meaning of some types. E.g I'm looking for bond type for simple double bond between C=C as well as C=N ( here both atoms in 5-m ring) atoms pairs. Should I use for the first one #define gb_15 0.1390 8.6600e+06 ; CH2 - C, CR1 (6-ring) 800 and for the second one ; #define gb_11 0.1340 1.0500e+07 ; C - N, NZ, NE 900 ? Neither. gb_10 sounds exactly like what you need: #define gb_10 0.1330 1.1800e+07 ; C, CR1 - N, NR, CR1, C (peptide, 5-ring) 1000 -Justin -- ==__== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist 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] parameters for bond types for GROMOS force field.
Justin, thanks alot. I'll try to use gb_10 ( for C=N) as well as gb_16 ( for C=C) for parametrisation in my task. James 2012/6/8 Justin A. Lemkul jalem...@vt.edu On 6/8/12 2:01 PM, James Starlight wrote: Justin, Does the gb_10 suitable for both bonds that I want to parametrise ? As I've told previously I need to parametrise two different bonds 1) is the C=C bond wich are not in the ring. This is just double bound in linnear sequence -C=C-. 2) is the C=N- double bond where both atoms in the 5-m ring system This is a better description. The last message suggested everything was in a 5-membered ring. Had that been the case, my suggestion would have been right (see, for instance, a HIS side chain - gb_10 is used for both C=C and C=N in that case). There are no linear C=C bonds in Gromos force fields by default, as such groups are not in proteins. The closest you can likely come is to take a C=C bond from the PHE ring. Bond lengths are simple, and are usually derived from spectroscopic information. If using constraints on all bonds, the force constant is irrelevant since the bond is rigid. If not using constraints, then you'll have to find or derive suitable parameters yourself. Welcome to the inconvenient world of parameterization :) -Justin Thanks again, James 2012/6/8 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu On 6/8/12 1:22 PM, James Starlight wrote: I've found that information in ffbonded.itp but I'm not sure about exactly meaning of some types. E.g I'm looking for bond type for simple double bond between C=C as well as C=N ( here both atoms in 5-m ring) atoms pairs. Should I use for the first one #define gb_15 0.1390 8.6600e+06 ; CH2 - C, CR1 (6-ring) 800 and for the second one ; #define gb_11 0.1340 1.0500e+07 ; C - N, NZ, NE 900 ? Neither. gb_10 sounds exactly like what you need: #define gb_10 0.1330 1.1800e+07 ; C, CR1 - N, NR, CR1, C (peptide, 5-ring) 1000 -Justin -- ==**__== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing list gmx-users@gromacs.org mailto: gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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
