Piggot T. <T.Piggot@...> writes: > > 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-bounces@... > [gromacs.org_gmx-users-bounces@...] on behalf > of Michael Carter [Michael.Carter@...] > Sent: 20 August 2014 12:56 > To: gmx-users@... > 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" <bipinelmat@...> 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.Carter@...> > >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-request@... > >> > >-- > >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-request@... > > 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-request@...
Hi, Related to the Zn-parameters; where can I find the reference (author, journal, year) to the sigma and epsilon (1.95998e-01 5.23000e-02) parameters that I find in /gromacs/top/amber99sb.ff/ffnonbonded.itp for [ atomtypes ] Zn. I would like to use amber99sb force field in my Gromacs simulation of a Zn- containing protein. Best regards, Emma +++++++++++++++++++++++++ Join us for an exciting international meeting in Kalmar - http://ccbglinnaeus.wix.com/swedtheorchem2015 ----------------------------------------------------------- Emma Ahlstrand PhD student Linnaeus University Faculty of Health and Life Sciences 391 82 Kalmar / 351 95 Växjö Sweden +46 772 28 80 00 Telephone exchange +46 480 44 61 52 Direct +46 739 05 71 86 Mobile emma.ahlstr...@lnu.se http://lnu.se/ccbg Lnu.se Challenging educations. Prominent research. Linnaeus University – a modern, international university in Småland, Sweden. -- 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.