[gmx-users] Serine phosphorylation

[Peter Stern]

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
> 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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