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
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