Yes, Peter is right. I was assuming the residue S2P is already in the amber force field. If not, you can use the phosphoserine parameters derived by Homeyer and co-workers <http://rd.springer.com/article/10.1007%2Fs00894-005-0028-4> and distributed in the AMBER parameter database <http://sites.pharmacy.manchester.ac.uk/bryce/amber/>, and follow Peter's suggestions.
Cheers, On 10 January 2016 at 10:13, Peter Stern <peter.st...@weizmann.ac.il> wrote: > The instructions for adding a new residue are here: > > http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field?highlight=add+new+residue > > If you cannot understand these instructions, then most probably you will > have to read about them in Chapter 5 of the gromacs manual in order to > understand what all the different files mentioned are about. In > particular, you will have to define a new residue, e.g. SERP or something > like that in the residuetypes.dat file, but also in the aminoacids.rtp > file making sure that all the new bonds, angles and dihedrals are defined > and that these also exist in the ffbonded.itp file. The biggest challenge > will be assigning the correct charges to the atoms of the new residue so > that the net charge is now, for example, -1. One way to do this is to run > Gaussian. You need to google this a bit. > > Regards, > Peter > > -----Original Message----- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Simone > Bolognini > Sent: Sunday, January 10, 2016 11:08 AM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Serine phosphorylation > > Thank you for your support, but I find the instructions on the website > extremely unclear to me. There are some commands to be run which are nor > gromacs neither bash commands that pretty puzzle me. However, I'd better be > more specific in explaining my problem: I have a protein whose pdb contains > a particular serine in which I am interested on. Now, for some reasons, I > need to change this serine (and only this one!) to a phosphorylated one and > run some MD production using AMBER-ILDN with this new configuration. What > should I do exactly? Can you provide me a sequence of steps which I should > follow in order to go from the starting pdb to the actual simulation? > > As always, thank you very much for your help! > Simone > > Il giorno ven 8 gen 2016 alle ore 13:30 Changrong Ge < > changrong...@gmail.com> ha scritto: > > > http://selene.princeton.edu/FFPTM/ > > > > On Fri, Jan 8, 2016 at 9:52 AM, Simone Bolognini > > <simo.bologn...@gmail.com > > > > > wrote: > > > > > Hi everyone, > > > I need to run some MD simulations with a protein where a particular > > serine > > > should be phosphorylated. Since in the original pdb the serine is > > actually > > > not, I guess I should modify something 'by hand'. I'm going to use > > > AMBER-ILDN ff. Can anyone of you tell me what should I do? My first > > > guess was to generate the topology and then directly substitute my > > > serine with the phosphorylated one (looking for the AMBER-ILDN > > > parameters), but sincerely I don't know if this is the correct way to > proceed. > > > > > > Thanks a lot for your support! > > > Simone > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? 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