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AMBER Archive (2004)Subject: RE: AMBER: a question on MM-PBSA and Delphi
From: Jiayun (jxp251_at_bham.ac.uk)
Hi Thomas,
When my mmpbsa run crashed, it gave me the error message
"sh: /SW/delphi: cannot execute
/SW/delphi delphi.prm.0 > ras_raf_II_wt_com.delphilog.1.0 not
I had only one link "fort.13 -> ras_raf_II_wt_com.pdb.1" generated. The
"MM
GB
PB
MS
1
BOND = 693.4575 ANGLE = 1895.7111 DIHED =
VDWAALS = -1974.0288 EEL = -17194.5212 EGB =
1-4 VDW = 866.5634 1-4 EEL = 7173.9328 RESTRAINT =
The following part was missed compared to the example run.
"corrected reaction field energy: 0.0000 kt
corrected reaction field energy: -6897.185 kt
surface area = 11380.021"
So it seems Delphi didn't work properly. Then I used the same pdb file to
Any further suggestions will be much appreciated.
Jiayun
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