Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated residues
Hi, QM parameterisation is how people tend to have done it for things like copper-bound proteins with GROMOS. I have been recently simulating one of these copper-bound proteins using a GROMOS force field (and indeed an AMBER force field too). I can send you a couple of papers regarding the GROMOS parameterisation for this protein off list if you like, so you can at least see their parameterisation methods for the copper centre? Cheers Tom From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Michael Carter [michael.car...@icr.ac.uk] Sent: 21 August 2014 13:10 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated residues Hi Tom, Thanks, I will look into it. I know AMBER has the ZAFF forcefield, and I have done the simulation in AMBER, but I wanted to know if GROMOS forcefields have this capability. I will have a play and see what I can do, most likely I will do a small QM/MM run and use this to parameterise the Zinc ions. Thanks for the help. Cheers, Mike From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Piggot T. [t.pig...@soton.ac.uk] Sent: Wednesday, August 20, 2014 4:46 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated residues Hi Mike, As well as the link that Bipin sent, you can also get parameters for GROMOS phosphorylated residues (compatible with the 43A1 force field, I think) from: http://www.gromacs.org/Downloads/User_contributions/Force_fields I've never used either so have no idea which might be better. The ones that Binpin suggested look like they work with the newer GROMOS 54A7 force field, so they might be the ones to use. On your other question, I am not sure about the protein-zinc parameters with a GROMOS force field. I would say, is there any particular need for using one of the GROMOS protein force fields? There are definitely parameters out there for some of the all-atom protein force fields (e.g. AMBER ones) which are probably also better in terms of protein parameters. Cheers Tom PS: Hope things are good in the (relatively) new job! From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Michael Carter [michael.car...@icr.ac.uk] Sent: 20 August 2014 12:56 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated residues Hi Bipin, Thanks for this. It works well for adding functionality to residues. Cheers, Mike Carter On 20/08/2014 12:10, bipin singh bipinel...@gmail.com wrote: This might help. http://vienna-ptm.univie.ac.at/ *Thanks and Regards,Bipin Singh* On Wed, Aug 20, 2014 at 4:30 PM, Michael Carter michael.car...@icr.ac.uk wrote: Hi, I have two questions regarding the parameterisation of Zinc ions and a phosphorylated TYR residue within two different protein systems. 1. Zinc parameters: I have three zinc ions within one protein system. I want to use a bonded model so that they do not fly out of my protein upon simulation. Is there any documentation on the parameters for such a model in the GROMOS forcefield? 2. Phosphorylated TYR In another system I have a phosphorylated TYR residue. PDB2GMX does not like this and after looking inot the manual I have found that you can add parameters for this to the existing forcefields. Much like the previous question, is there any documentation on the addition of parameters for phosphorylated residues in the GROMOS forcefield? Any pointers for these questions would be greatly appreciated. Cheers, Mike Carter The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https
[gmx-users] Forcefield parameters for Zinc and phosphorylated residues
Hi, I have two questions regarding the parameterisation of Zinc ions and a phosphorylated TYR residue within two different protein systems. 1. Zinc parameters: I have three zinc ions within one protein system. I want to use a bonded model so that they do not fly out of my protein upon simulation. Is there any documentation on the parameters for such a model in the GROMOS forcefield? 2. Phosphorylated TYR In another system I have a phosphorylated TYR residue. PDB2GMX does not like this and after looking inot the manual I have found that you can add parameters for this to the existing forcefields. Much like the previous question, is there any documentation on the addition of parameters for phosphorylated residues in the GROMOS forcefield? Any pointers for these questions would be greatly appreciated. Cheers, Mike Carter The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated residues
This might help. http://vienna-ptm.univie.ac.at/ *Thanks and Regards,Bipin Singh* On Wed, Aug 20, 2014 at 4:30 PM, Michael Carter michael.car...@icr.ac.uk wrote: Hi, I have two questions regarding the parameterisation of Zinc ions and a phosphorylated TYR residue within two different protein systems. 1. Zinc parameters: I have three zinc ions within one protein system. I want to use a bonded model so that they do not fly out of my protein upon simulation. Is there any documentation on the parameters for such a model in the GROMOS forcefield? 2. Phosphorylated TYR In another system I have a phosphorylated TYR residue. PDB2GMX does not like this and after looking inot the manual I have found that you can add parameters for this to the existing forcefields. Much like the previous question, is there any documentation on the addition of parameters for phosphorylated residues in the GROMOS forcefield? Any pointers for these questions would be greatly appreciated. Cheers, Mike Carter The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated residues
Hi Bipin, Thanks for this. It works well for adding functionality to residues. Cheers, Mike Carter On 20/08/2014 12:10, bipin singh bipinel...@gmail.com wrote: This might help. http://vienna-ptm.univie.ac.at/ *Thanks and Regards,Bipin Singh* On Wed, Aug 20, 2014 at 4:30 PM, Michael Carter michael.car...@icr.ac.uk wrote: Hi, I have two questions regarding the parameterisation of Zinc ions and a phosphorylated TYR residue within two different protein systems. 1. Zinc parameters: I have three zinc ions within one protein system. I want to use a bonded model so that they do not fly out of my protein upon simulation. Is there any documentation on the parameters for such a model in the GROMOS forcefield? 2. Phosphorylated TYR In another system I have a phosphorylated TYR residue. PDB2GMX does not like this and after looking inot the manual I have found that you can add parameters for this to the existing forcefields. Much like the previous question, is there any documentation on the addition of parameters for phosphorylated residues in the GROMOS forcefield? Any pointers for these questions would be greatly appreciated. Cheers, Mike Carter The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated residues
Hi Mike, As well as the link that Bipin sent, you can also get parameters for GROMOS phosphorylated residues (compatible with the 43A1 force field, I think) from: http://www.gromacs.org/Downloads/User_contributions/Force_fields I've never used either so have no idea which might be better. The ones that Binpin suggested look like they work with the newer GROMOS 54A7 force field, so they might be the ones to use. On your other question, I am not sure about the protein-zinc parameters with a GROMOS force field. I would say, is there any particular need for using one of the GROMOS protein force fields? There are definitely parameters out there for some of the all-atom protein force fields (e.g. AMBER ones) which are probably also better in terms of protein parameters. Cheers Tom PS: Hope things are good in the (relatively) new job! From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Michael Carter [michael.car...@icr.ac.uk] Sent: 20 August 2014 12:56 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated residues Hi Bipin, Thanks for this. It works well for adding functionality to residues. Cheers, Mike Carter On 20/08/2014 12:10, bipin singh bipinel...@gmail.com wrote: This might help. http://vienna-ptm.univie.ac.at/ *Thanks and Regards,Bipin Singh* On Wed, Aug 20, 2014 at 4:30 PM, Michael Carter michael.car...@icr.ac.uk wrote: Hi, I have two questions regarding the parameterisation of Zinc ions and a phosphorylated TYR residue within two different protein systems. 1. Zinc parameters: I have three zinc ions within one protein system. I want to use a bonded model so that they do not fly out of my protein upon simulation. Is there any documentation on the parameters for such a model in the GROMOS forcefield? 2. Phosphorylated TYR In another system I have a phosphorylated TYR residue. PDB2GMX does not like this and after looking inot the manual I have found that you can add parameters for this to the existing forcefields. Much like the previous question, is there any documentation on the addition of parameters for phosphorylated residues in the GROMOS forcefield? Any pointers for these questions would be greatly appreciated. Cheers, Mike Carter The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
