[gmx-users] Serine phosphorylation

[Simone Bolognini]

Thank you Catarina and Peter! This will help me very much. So, I manually
phosphorylated my serine using the pymol plugin PyTM's. Then I manually
modified the name of my serine from SER to S2P in the pdb file and tried to
compute the topology via AMBER-ILDN. As expected, it didn't work. So I
started adding the S2P residue, as Peter reported. However, I'm having some
troubles in interpreting the database. I got the charges correctly (they
sum to -2 so I suppose they are correct) but I cannot find the bonds,
dihedrals and impropers which are required in the aminoacids.rtp file. Do
you know how can I do?

Thank you again! Your support is priceless.
Simone

Il giorno dom 10 gen 2016 alle ore 13:09 Catarina A. Carvalheda dos Santos <
c.a.c.dossantos at dundee.ac.uk> ha scritto:

> 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.stern at 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-bounces at maillist.sys.kth.se [mailto:
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Simone
> > Bolognini
> > Sent: Sunday, January 10, 2016 11:08 AM
> > To: gmx-users at 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.ge at gmail.com> ha scritto:
> >
> > > http://selene.princeton.edu/FFPTM/
> > >
> > > On Fri, Jan 8, 2016 at 9:52 AM, Simone Bolognini
> > > <simo.bolognini at 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
> > > > --
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> > >
> > >
> > >
> > > --
> > >
> > > Changrong Ge, PhD
> > >
> > > Division of Medical Inflammation Research Department of Medical
> > > Biochemistry and Biophysics (MBB) Karolinska Institutet Scheeles väg
> > > 2, B2 Plan 4
> > > SE-171 77 Stockholm
> > > Sweden
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> --
> Catarina A. Carvalheda
>
> PhD Student
> Computational Biology Division
> SSE & SLS
> University of Dundee
> DD1 5EH, Dundee, Scotland, UK
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