From: Nehad Elsalamouny (nehade_at_uow.edu.au)
Date: Fri Dec 15 2017 - 23:53:33 CST
Dear namd users,
I am running a FEP calculation (20 windows, at lambda = 0.00-0.05, 0.05-0.10,….. 0.95-1.00 both forward and backward) perturbing protein residue 146 from serine to glutamic acid (S2E).
Here is the part of pdb file showing residue 146 (serine).
ATOM 1142 N SER U 146 -25.001 -24.526 2.605 1.00 22.58 N
ATOM 1143 CA SER U 146 -25.081 -23.133 2.931 1.00 23.53 C
ATOM 1144 CB SER U 146 -26.354 -22.782 3.695 1.00 23.70 C
ATOM 1145 OG SER U 146 -27.478 -23.144 2.998 1.00 23.44 O
ATOM 1146 C SER U 146 -23.888 -22.752 3.786 1.00 25.14 C
ATOM 1147 O SER U 146 -23.435 -21.662 3.617 1.00 26.16 O
Here is the part of pdb file I use as an input to generate the psf file (serine to glutamic acid):
ATOM 1142 NA S2E U 146 -25.001 -24.526 2.605 1.00 22.58 N
ATOM 1143 CAA S2E U 146 -25.081 -23.133 2.931 1.00 23.53 C
ATOM 1144 CBA S2E U 146 -26.354 -22.782 3.695 1.00 23.70 C
ATOM 1145 OGA S2E U 146 -27.478 -23.144 2.998 1.00 23.44 O
ATOM 1146 CA S2E U 146 -23.888 -22.752 3.786 1.00 25.14 C
ATOM 1147 OA S2E U 146 -23.435 -21.662 3.617 1.00 26.16 O
ATOM 1143 CAB S2E U 146 -25.081 -23.133 2.931 1.00 23.53 C
ATOM 1144 CBB S2E U 146 -26.354 -22.782 3.695 1.00 23.70 C
ATOM 1146 CB S2E U 146 -23.888 -22.752 3.786 1.00 25.14 C
ATOM 1147 OB S2E U 146 -23.435 -21.662 3.617 1.00 26.16 O
ATOM 1142 NB S2E U 146 -25.001 -24.526 2.605 1.00 22.58 N
On running the simulation, most lambda values ran fine, however, I get an error message for some lambda values after running for some time.
FATAL ERROR: Bad global improper count! (798 vs 799)
I read from previous emails, it could be a bad initial structure however I am not sure what is the problem in my case.
Thanks for your help,
Nehad
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