AMBER Archive (2007)

Subject: AMBER: WARNING: Missing VDWNB for MM in 1 -> Taken from 0

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• Previous message: David A. Case: "Re: AMBER: error when using sander.LES: exceeded MAXLES"
• In reply to: saurabh agrawal: "AMBER: vertex atom mismatch"
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Dear Friend,
while running mm-pbsa for binding energy calculation i
am getting following error. i have checked the mail
archive and i made coordinate file top file many time
but this error is still same with vertex as i have
given in the previous mail.

*****************************************
vertex atom mismatch
       atom: 31
vertex atom: 29
vertex atom mismatch
       atom: 31
vertex atom: 29
***********************************************

WARNING: Missing VDWNB for MM in 1 -> Taken from 0
    WARNING: Missing ANGLE for MM in 1 -> Taken from 0
    WARNING: Missing VDW14 for MM in 2 -> Taken from 1
    WARNING: Missing VDWNB for MM in 2 -> Taken from 1
    WARNING: Missing ANGLE for MM in 2 -> Taken from 1
    WARNING: Missing SURF for MS in 2 -> Taken from 1
    WARNING: Missing ELE14 for MM in 3 -> Taken from 2
    WARNING: Missing VDW14 for MM in 3 -> Taken from 2
    WARNING: Missing ANGLE for MM in 3 -> Taken from 2
    WARNING: Missing SURF for MS in 3 -> Taken from 2
    WARNING: Missing ELE14 for MM in 4 -> Taken from 3
    WARNING: Missing ELENB for MM in 4 -> Taken from 3
    WARNING: Missing VDW14 for MM in 4 -> Taken from 3
    WARNING: Missing VDWNB for MM in 4 -> Taken from 3
    WARNING: Missing ANGLE for MM in 4 -> Taken from 3
    WARNING: Missing SURF for MS in 4 -> Taken from 3
    WARNING: Missing ELE14 for MM in 5 -> Taken from 4
    WARNING: Missing ELENB for MM in 5 -> Taken from 4
    WARNING: Missing VDW14 for MM in 5 -> Taken from 4
    WARNING: Missing VDWNB for MM in 5 -> Taken from 4
    WARNING: Missing ANGLE for MM in 5 -> Taken from 4
    WARNING: Missing SURF for MS in 5 -> Taken from 4
    WARNING: Missing ELE14 for MM in 6 -> Taken from 5
    WARNING: Missing VDW14 for MM in 6 -> Taken from 5
    WARNING: Missing ANGLE for MM in 6 -> Taken from 5
    WARNING: Missing ELE14 for MM in 7 -> Taken from 6
    WARNING: Missing ELENB for MM in 7 -> Taken from 6
    WARNING: Missing VDW14 for MM in 7 -> Taken from 6
    WARNING: Missing VDWNB for MM in 7 -> Taken from 6
    WARNING: Missing SURF for MS in 7 -> Taken from 6
    WARNING: Missing ELENB for MM in 8 -> Taken from 7
    WARNING: Missing VDW14 for MM in 8 -> Taken from 7
    WARNING: Missing VDWNB for MM in 8 -> Taken from 7
    WARNING: Missing ELE14 for MM in 9 -> Taken from 8
    WARNING: Missing VDW14 for MM in 9 -> Taken from 8
    WARNING: Missing VDWNB for MM in 9 -> Taken from 8
    WARNING: Missing ELE14 for MM in 10 -> Taken from
9
    WARNING: Missing ELENB for MM in 10 -> Taken from
9
    WARNING: Missing VDW14 for MM in 10 -> Taken from
9
    WARNING: Missing VDWNB for MM in 10 -> Taken from
9
    WARNING: Missing SURF for MS in 10 -> Taken from 9
    WARNING: Missing ELENB for MM in 11 -> Taken from
10
    WARNING: Missing VDWNB for MM in 11 -> Taken from
10
    WARNING: Missing SURF for MS in 11 -> Taken from
10
    WARNING: Missing ELE14 for MM in 12 -> Taken from
11
    WARNING: Missing VDW14 for MM in 12 -> Taken from
11
    WARNING: Missing VDWNB for MM in 12 -> Taken from
11
    WARNING: Missing ELENB for MM in 13 -> Taken from
12
    WARNING: Missing VDW14 for MM in 13 -> Taken from
12
    WARNING: Missing VDWNB for MM in 13 -> Taken from
12
    WARNING: Missing ELE14 for MM in 14 -> Taken from
13
    WARNING: Missing ELENB for MM in 14 -> Taken from
13
    WARNING: Missing VDW14 for MM in 14 -> Taken from
13
    WARNING: Missing VDWNB for MM in 14 -> Taken from
13
    WARNING: Missing SURF for MS in 14 -> Taken from
13
    WARNING: Missing ELE14 for MM in 15 -> Taken from
14
    WARNING: Missing VDW14 for MM in 15 -> Taken from
14
    WARNING: Missing VDWNB for MM in 15 -> Taken from
14
    WARNING: Missing SURF for MS in 15 -> Taken from
14
    WARNING: Missing ELE14 for MM in 16 -> Taken from
15
    WARNING: Missing ELENB for MM in 16 -> Taken from
15
    WARNING: Missing VDW14 for MM in 16 -> Taken from
15
    WARNING: Missing VDWNB for MM in 16 -> Taken from
15
    WARNING: Missing ANGLE for MM in 16 -> Taken from
15
    WARNING: Missing VDW14 for MM in 17 -> Taken from
16
    WARNING: Missing VDWNB for MM in 17 -> Taken from
16
    WARNING: Missing ANGLE for MM in 17 -> Taken from
16
    WARNING: Missing ELENB for MM in 18 -> Taken from
17
    WARNING: Missing VDWNB for MM in 18 -> Taken from
17
    WARNING: Missing ELE14 for MM in 19 -> Taken from
18
    WARNING: Missing VDW14 for MM in 19 -> Taken from
18
    WARNING: Missing VDWNB for MM in 19 -> Taken from
18
    WARNING: Missing ANGLE for MM in 19 -> Taken from
18
    Reading telo_rec.all.out
    Checking CALC
    WARNING: Missing VDWNB for MM in 1 -> Taken from 0
    WARNING: Missing ANGLE for MM in 1 -> Taken from 0
    WARNING: Missing VDW14 for MM in 2 -> Taken from 1
    WARNING: Missing VDWNB for MM in 2 -> Taken from 1
    WARNING: Missing ANGLE for MM in 2 -> Taken from 1
    WARNING: Missing SURF for MS in 2 -> Taken from 1
    WARNING: Missing ELE14 for MM in 3 -> Taken from 2
    WARNING: Missing VDW14 for MM in 3 -> Taken from 2
    WARNING: Missing ANGLE for MM in 3 -> Taken from 2
    WARNING: Missing SURF for MS in 3 -> Taken from 2
    WARNING: Missing ELE14 for MM in 4 -> Taken from 3
    WARNING: Missing ELENB for MM in 4 -> Taken from 3
    WARNING: Missing VDW14 for MM in 4 -> Taken from 3
    WARNING: Missing VDWNB for MM in 4 -> Taken from 3
    WARNING: Missing ANGLE for MM in 4 -> Taken from 3
    WARNING: Missing SURF for MS in 4 -> Taken from 3
    WARNING: Missing ELE14 for MM in 5 -> Taken from 4
    WARNING: Missing ELENB for MM in 5 -> Taken from 4
    WARNING: Missing VDW14 for MM in 5 -> Taken from 4
    WARNING: Missing VDWNB for MM in 5 -> Taken from 4
    WARNING: Missing ANGLE for MM in 5 -> Taken from 4
    WARNING: Missing SURF for MS in 5 -> Taken from 4
    WARNING: Missing ELE14 for MM in 6 -> Taken from 5
    WARNING: Missing VDW14 for MM in 6 -> Taken from 5
    WARNING: Missing ANGLE for MM in 6 -> Taken from 5
    WARNING: Missing ELE14 for MM in 7 -> Taken from 6
    WARNING: Missing ELENB for MM in 7 -> Taken from 6
    WARNING: Missing VDW14 for MM in 7 -> Taken from 6
    WARNING: Missing VDWNB for MM in 7 -> Taken from 6
    WARNING: Missing SURF for MS in 7 -> Taken from 6
    WARNING: Missing ELENB for MM in 8 -> Taken from 7
    WARNING: Missing VDW14 for MM in 8 -> Taken from 7
    WARNING: Missing VDWNB for MM in 8 -> Taken from 7
    WARNING: Missing ELE14 for MM in 9 -> Taken from 8
    WARNING: Missing VDW14 for MM in 9 -> Taken from 8
    WARNING: Missing VDWNB for MM in 9 -> Taken from 8
    WARNING: Missing ELE14 for MM in 10 -> Taken from
9
    WARNING: Missing ELENB for MM in 10 -> Taken from
9
    WARNING: Missing VDW14 for MM in 10 -> Taken from
9
    WARNING: Missing VDWNB for MM in 10 -> Taken from
9
    WARNING: Missing SURF for MS in 10 -> Taken from 9
    WARNING: Missing ELENB for MM in 11 -> Taken from
10
    WARNING: Missing VDWNB for MM in 11 -> Taken from
10
    WARNING: Missing SURF for MS in 11 -> Taken from
10
    WARNING: Missing ELE14 for MM in 12 -> Taken from
11
    WARNING: Missing VDW14 for MM in 12 -> Taken from
11
    WARNING: Missing VDWNB for MM in 12 -> Taken from
11
    WARNING: Missing ELENB for MM in 13 -> Taken from
12
    WARNING: Missing VDW14 for MM in 13 -> Taken from
12
    WARNING: Missing VDWNB for MM in 13 -> Taken from
12
    WARNING: Missing ELE14 for MM in 14 -> Taken from
13
    WARNING: Missing ELENB for MM in 14 -> Taken from
13
    WARNING: Missing VDW14 for MM in 14 -> Taken from
13
    WARNING: Missing VDWNB for MM in 14 -> Taken from
13
    WARNING: Missing SURF for MS in 14 -> Taken from
13
    WARNING: Missing ELE14 for MM in 15 -> Taken from
14
    WARNING: Missing VDW14 for MM in 15 -> Taken from
14
    WARNING: Missing VDWNB for MM in 15 -> Taken from
14
    WARNING: Missing SURF for MS in 15 -> Taken from
14
    WARNING: Missing ELE14 for MM in 16 -> Taken from
15
    WARNING: Missing ELENB for MM in 16 -> Taken from
15
    WARNING: Missing VDW14 for MM in 16 -> Taken from
15
    WARNING: Missing VDWNB for MM in 16 -> Taken from
15
    WARNING: Missing ANGLE for MM in 16 -> Taken from
15
    WARNING: Missing VDW14 for MM in 17 -> Taken from
16
    WARNING: Missing VDWNB for MM in 17 -> Taken from
16
    WARNING: Missing ANGLE for MM in 17 -> Taken from
16
    WARNING: Missing ELENB for MM in 18 -> Taken from
17
    WARNING: Missing VDWNB for MM in 18 -> Taken from
17
    WARNING: Missing ELE14 for MM in 19 -> Taken from
18
    WARNING: Missing VDW14 for MM in 19 -> Taken from
18
    WARNING: Missing VDWNB for MM in 19 -> Taken from
18
    WARNING: Missing ANGLE for MM in 19 -> Taken from
18
    Reading telo_lig.all.out

saurabh

                
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• Next message: David A. Case: "Re: AMBER: perturbed atoms are not bonded on using TIP5P wate"
• Previous message: David A. Case: "Re: AMBER: error when using sander.LES: exceeded MAXLES"
• In reply to: saurabh agrawal: "AMBER: vertex atom mismatch"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]