[gmx-users] Force field parameters for phosphorylated tyrosine

[Peter C. Lai]

On 2011-06-13 08:33:15AM -0500, bharat gupta wrote:
> thanks for the reply...
> 
> Actually I have found the amber parameters for p-TYR from the following links : http://www.pharmacy.manchester.ac.uk/bryce/amber#pro
> 
> I am not able to how build the residue topology ..  shall I add the topology of phosphate only from this to normal tyrosine residue ??

> # Parameters for TYR-PO2(OH) : Y1P; N.Homeyer, A.H.C.Horn, H.Lanig, H.Sticht, J. Mol. Model., in press
> BOND
> OS - P   525.0   1.610
> OH - P   525.0   1.610
> 
> ANGLE
> C - OS - P   100.0   120.50
> O2 - P - OH  140.0   108.23
> HO - OH - P  140.0   108.50
> CA - C - OS   70.0   120.00
> 
> DIHE
> 
> IMPR
> CA-CA-C-OS    1.1     180.0      2.0
> 

You will need to figure out what atomtype corresponds to the Amber type.
Start with amberversion.ff/atomtypes.atp It is probably going to be P

Then copy the [ TYR ] section in amberversion.ff/aminoacids.rtp to say, 
[ TYP ] and patch the toplogy there. Make sure your charges are satisfied
(rule of thumb is if a carbon's going to lose a hydrogen in the new bond,
shift the previous charge of the hydrogen on to the carbon that's lost it).
The necessary bonds parameters appear to already exist in ffbonded.itp, 
however looking at amber99sb, the required angles and possible dihedrals are 
not there. You will have to patch those. I intuit that you mulitply the first 
amber angle term by 4.184 to get gromacs cth and the theta angle is the 2nd 
amber angle term. Not sure how to convert the improper dihedral though, 
however it looks like the 3rd amber improper term corresponds to the gromacs 
phase (180.0) and the last amber improper term corresponds to the phase
number (2); but I have no idea how to convert the 1.1 to gromacs kd, maybe
the person who did the amber conversions to gromacs knows what the formula
is.


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