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
running properly"
I had only one link "fort.13 -> ras_raf_II_wt_com.pdb.1" generated. The
ras_raf_II_wt_com.all.out file is like
"MM
GB
PB
MS
1
BOND = 693.4575 ANGLE = 1895.7111 DIHED =
1478.8198
VDWAALS = -1974.0288 EEL = -17194.5212 EGB =
-2773.2755
1-4 VDW = 866.5634 1-4 EEL = 7173.9328 RESTRAINT =
0.0000"
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
make two copies: one is called *.pdb and the other is *pdb.1 to run Delphi
directly. The Delphi with *.pdb file gave the output and generated a new pdb
with the assigned atomic radius and charge of each atom placed in columns
55-60 and 61-67 but the other one with the name *pdb.1 didn't generate the
new pdb file. So that's why I sent the first email, saying I think Delphi
could only recognise the file with pdb end.
Any further suggestions will be much appreciated.
Jiayun
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Received on Wed Jun 23 2004 - 19:53:01 PDT
