Dear Friends,
I am running MM-PBSA module with following ptraj input
file to genetare mdcrd file for snapshots.
____________________________________________
trajin md15/telo_md15.crd 50 75
strip :WAT
strip :K+
trajout snap_md15_10.mdcrd nobox
go
____________________________________________
When I run the output mdcrd file in VMD with the new
top file i made for complex it is running fine.
but after running mmpbsa.in of 01_Generatesnapshot
folder the generated snapshot eg telo_comp.crd.1 is
showing only dots in place of molecule.
When i run mmpbsa.in in 02_MMPBSA_Stability folder the
folloing message is comming.
____________________________________________
vertex atom mismatch
atom: 31
vertex atom: 29
vertex atom mismatch
atom: 31
vertex atom: 29
____________________________________________
And the following huge values of the results are
comming.
_______________________________________________
# -----------------------
----------------------- -----------------------
# MEAN STD MEAN
STD MEAN STD
# =======================
======================= =======================
ELE 2021.28 1055.18 2232.51
998.35 -26.91 87.09
VDW 92802868.21 55014441.20 91574617.24
55791565.05 7749606.10 13644989.88
INT 11856797.43 3899253.57 11682388.39
3879628.69 176838.10 87099.44
GAS 104661686.91 56685945.43 103259238.13
57407860.33 7926417.30 13663948.08
PBSUR 24.04 0.40 23.04
0.43 4.23 0.51
PBCAL -8599.31 1496.46 -8554.51
1470.67 -244.88 42.13
PBSOL -8575.28 1496.38 -8531.47
1470.47 -240.66 42.01
PBELE -6578.04 1882.76 -6322.00
1779.86 -271.79 70.85
PBTOT 104653111.64 56685881.92 103250706.66
57407828.31 7926176.64 13663947.99
GBSUR 24.04 0.40 23.04
0.43 4.23 0.51
GB -7727.20 902.87 -7647.03
952.07 -261.15 44.00
GBSOL -7703.17 902.72 -7623.99
952.09 -256.93 43.86
GBELE -5705.93 1015.97 -5414.52
971.33 -288.06 73.30
GBTOT 104653983.75 56685950.86 103251614.14
57407862.45 7926160.37 13663950.37
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -184.33 149.59
VDW -6521355.13 13572760.12
INT -2429.06 44961.67
GAS -6523968.52 13571215.99
PBSUR -3.23 0.39
PBCAL 200.08 261.03
PBSOL 196.85 261.15
PBELE 15.76 232.94
PBTOT -6523771.67 13571298.28
GBSUR -3.23 0.39
GB 180.98 123.21
GBSOL 177.75 123.34
GBELE -3.35 142.11
GBTOT -6523790.77 13571230.08
_________________________________________________
Please help me in solving this problem.
Thanking you.
saurabh
__________________________________________________________
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Received on Sun Jan 21 2007 - 06:07:17 PST
