[gmx-users] Serine phosphorylation

Wed Jan 13 07:51:15 CET 2016

 http://vienna-ptm.univie.ac.at/

On Mon, Jan 11, 2016 at 11:11 PM, Simone Bolognini <simo.bolognini at gmail.com
> wrote:

> Thank you! Putting every hint together made the thing work perfectly! Now,
> I would be interested in performing some trial simulations in implicit
> solvent. However, GROMACS tells me that also the GBSA parameters should be
> modified in order to accomodate the new phosphorylated residue. I looked
> EVERYWHERE in literature (I spent approximately 2h in the attempt) in order
> to find useful values of gbr and hct (gbsa.itp) for P and OS (sp3 O I
> guess), but they were nowhere to be found! Do you know where I can look for
> them?
>
> Thank you.
> Simone
> Il giorno dom 10 gen 2016 alle ore 16:03 Justin Lemkul <jalemkul at vt.edu>
> ha
> scritto:
>
> >
> >
> > On 1/10/16 9:46 AM, Simone Bolognini wrote:
> > > 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?
> > >
> >
> > Copy whatever is in SER, and modify for the phosphate as needed (remove
> > HG, add
> > O-P bonds).  pdb2gmx only needs the [ bonds ] in order to generate angles
> > and
> > dihedrals.
> >
> > -Justin
> >
> > > 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
> > >>>>> --
> > >>>>> Gromacs Users mailing list
> > >>>>>
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> > >>>>> posting!
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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
> > >>>> 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
> > >>>> --
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> > >>> --
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> > >>> 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
> > >> --
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> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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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
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