[gmx-users] Parameters for neutral phosho-amino acids

[Justin A. Lemkul]

Michael McGovern wrote:
> Hi everyone.  I'm doing some simulations of a phosphorylated peptide. 
>  Right now, I'm using the amber force field with some parameters that 
> were obtained for charged phosphorylated amino acids in a paper I found. 
>  Now I want to simulate uncharged phosphate groups, but the paper only 
> gave parameters for -1 and -2 charge states.  I'm stuck on this.  I'm 
> only missing two bond parameters.  They are the OH-P-OH angle and the 
> HO-OH-P-OH dihedral, where the atom type names are shown below:
> 

A quick look at ffamber99bon.itp gives:

O2  P   OH           1   108.230    376.560 ;
O2  P   O2           1   119.900   1171.520 ;
O2  P   OS           1   108.230    836.800 ;
OH  P   OS           1   102.600    376.560 ;
OS  P   OS           1   102.600    376.560 ;

Are none of these appropriate?

As for dihedrals, from ffamber99bon.itp:

X   OH  P   X     3     1.04600     3.13800     0.00000    -4.18400     0.00000 
     0.00000     ; JCC,7,(1986),230
X   OS  P   X     3     1.04600     3.13800     0.00000    -4.18400     0.00000 
     0.00000     ; JCC,7,(1986),230

Perhaps that reference will have more information as far as the suitability of 
these parameters.

>    O2 (-)
>    | |
> R-P-OH-HO
>    | |
>   O2
> (-1 charge)
> 
>    O2
>    | |
> R-P-OH-HO
>     |
>    OH
>     |
>    HO
> (neutral)
> 
> Is there some way of getting these parameters?  Once that is done, I 
> still would need to assign charges.  Does anyone have any idea what the 
> best way forward would be?  I would prefer to stay in the amber force 
> field, but if that's not possible I'm open to others.
> 

Using antechamber is your best bet.  See the relevant discussions within the 
last day or so (and in the list archive) about using antechamber with acpypi.

There are parameters for Gromos96 43a1 (Ser, Thr, Tyr in -1 and -2 forms), 
published some time ago in J. Mol. Biol.  These files were provided on the 
GROMACS site in the User Contributions section, but were formatted for use with 
version 3.1.4.  I re-formatted them and have them available if you want to use 
them under version 4.0.x.  Just contact me off-list and I will send you the tarball.

-Justin

> Thanks for your time!
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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