[gmx-users] Serine phosphorylation

Sun Jan 10 16:03:08 CET 2016

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
>>>>>
>>>>> * 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
>> --
>> 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.

-- 
==================================================

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

==================================================