[gmx-users] Serine phosphorylation

Mon Jan 11 23:12:09 CET 2016

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
> >>>>> --
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> >>>>>
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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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> >>>
> >>
> >>
> >>
> >> --
> >> 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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