[gmx-users] fep calculation of L-Asn - D-Asn transition

[Alexandra Patriksson]

Dear all,

I'm trying to do a fep calculation of the L to D transition of a amino 
acid in a small peptide. We have done some changes to the dihedrals and 
the charges in the topology file (see below), but still we get 
dH/dlambda values that are far too large. Does anyone have an idea what 
could possibly be wrong? Have we forgotten something that should have 
been taken into account?

Our changes in the toplogy file going from L -> 0 :

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  
typeB    chargeB      massB
     7  opls_293B      1    ASN     CA      2       0.25     13.019     
opls_293B       0       13.019  ; qtot 0.94
     8   opls_140      1    ASN     HA      2       0.06          0     
opls_140        0       0       ; qtot 1
     9   opls_136      1    ASN     CB      3      -0.12     14.027     
opls_136        0       14.027  ; qtot 0.88
    10   opls_140      1    ASN    HB1      3       0.06          0     
opls_140        0       0       ; qtot 0.94
    11   opls_140      1    ASN    HB2      3       0.06          0     
opls_140        0       0       ; qtot 1

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            
c2            c3
    7    17     3     8     2            35             0             
0             200
    7    17     3     9     2            -35            0             
0             200


Our changes in the toplogy file going from 0 -> D :

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  
typeB    chargeB      massB
     7  opls_293B      1    ASN     CA      2          0     13.019     
opls_293B       0.25     13.019   ; qtot 0.94
     8   opls_140      1    ASN     HA      2          0          0     
opls_140        0.06          0   ; qtot 1
     9   opls_136      1    ASN     CB      3          0     14.027     
opls_136       -0.12     14.027   ; qtot 0.88
    10   opls_140      1    ASN    HB1      3          0          0     
opls_140        0.06          0   ; qtot 0.94
    11   opls_140      1    ASN    HB2      3          0          0     
opls_140        0.06          0   ; qtot 1

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            
c2            c3
    7    17     3     8     2             0             200           
-35           0
    7    17     3     9     2             0             200           
35            0



Thanks
Alexandra