[gmx-users] Re: phosphotyrosine

[Graham Smith]

I'm nearly there making topologies for phosophoserine, -tyrosine and
-threonine; I have files that build normally with pdb2gmx and grompp and
look OK after short MD. There are a couple of things I want to check first
though -

By analogy with the supplied dna bases I have put in two dihedral terms 
for the connection of the phosphate to the protein
eg 

[ SEP ]
...
 [ dihedrals ]
...
   CB    OG     P   O1P     gd_9
   CB    OG     P   O1P     gd_11

is this correct? One of these has multiplicity 2, one 3. 
So it would make sense if there's double bond character I guess. 

To use Hansson, Nordlund and Aqvist's parameters I had to introduce a new
atom type OP. I let gromacs use the normal Cij = sqrt(Cii Cjj) combination
rules for normal LJ, which was what Hansson et al did, but I seemed to
need explicit combination rules for LJ-14 if I was not to get zeros, so I
just used the same ones as for OA. Seem OK?

-Graham 

########################################################################

Dr. Graham R. Smith, 		       Department of Biological Sciences,  
Biomolecular Modelling Laboratory,     Biochemistry Building,              	
Cancer Research UK, 		       Imperial College of Science,        	
44 Lincoln's Inn Fields, 	        Technology & Medicine,             	
London WC2A 3PX,		       London SW7 2AZ,                     	
U.K. 				       U.K.                                	
Tel: +44-(0)20 7269 3348 	       Tel: +44-(0)20 7594 5734            	
email: graham.smith at cancer.org.uk	
URL: http://www.bmm.icnet.uk/~smithgr