[gmx-users] Serine phosphorylation

Catarina A. Carvalheda dos Santos c.a.c.dossantos at dundee.ac.uk
Sun Jan 10 13:08:52 CET 2016


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
> > > --
> > > 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 at gromacs.org.
> > >
> >
> >
> >
> > --
> >
> > 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
> > Tel:  +46-8-524 86337 ,   Mobile: +46-(0)76-2878 029
> > Fax: +46-8-524 87750 ,  Email: changrong.ge at ki.se
> > <changrong at dbb.su.se> or changrong.ge at gmail.com
> > --
> > 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 at 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-request at 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-request at gromacs.org.
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>



-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
SSE & SLS
University of Dundee
DD1 5EH, Dundee, Scotland, UK


More information about the gromacs.org_gmx-users mailing list