Hi Anju,
antechamber worked fine for me the way you used it with your pdb file.
antechamber -i mtx.pdb -fi pdb -o mtx.prepi -fo prepi -c bcc -s 2
Running: /share/apps/amber9_lampath/exe/bondtype -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full
Running: /share/apps/amber9_lampath/exe/atomtype -i ANTECHAMBER_AC.AC0
-o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 236; net charge: 0
Running: $AMBERHOME/exe/divcon
Running: /share/apps/amber9_lampath/exe/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/share/apps/amber9_lampath/dat/antechamber/BCCPARM.DAT -s 2 -j 1
Running: /share/apps/amber9_lampath/exe/atomtype -f ac -p bcc -o
ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
Running: /share/apps/amber9_lampath/exe/atomtype -i ANTECHAMBER_PREP.AC0
-o ANTECHAMBER_PREP.AC -p gaff
Running: /share/apps/amber9_lampath/exe/prepgen -i ANTECHAMBER_PREP.AC
-f int -o mtx.prepi -rn " " -rf molecule.res
Can it be that you have not set your $AMBERHOME?
Benjamin
Anju Sharma schrieb:
> Hi everybody
> while running antechamber in order to generate "prep" input file m
> getting following error:
>
> [root.amber MTX]# /usr/local/amber8/exe/antechamber -i
> /usr/local/Anju/Project/MTX/mtx.pdb -fi pdb -o
> /usr/local/Anju/Project/MTX/mtx.prepin -fo prepi -c bcc -s 2
> Cannot open CONNECT.TPL , exit
>
> i hv looked this CONNECT.TPL file which is present in dat/antechamber
> dir, bt unable to get nythng. Please help me in solving this problem,
> m enlcosing my pdb file for refernce in case if dere is ny problem wth
> my pdb file.
>
> waiting for early response as all my wrk is at halt jst coz of this
> problem
>
> --
> Anju Sharma
> Project Fellow,
> NIT, Hamirpur (H.P.)
0 0 2
This is a remark line
molecule.res
MTX INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 O13 oh M 3 2 1 1.540 111.208 180.000 -0.58984
5 H45 ho E 4 3 2 0.967 123.504 -3.696 0.39854
6 C12 c3 M 4 3 2 1.429 100.935 -122.421 0.13247
7 H43 h1 E 6 4 3 1.090 109.514 -169.764 0.02495
8 H44 h1 E 6 4 3 1.090 109.513 70.183 0.02313
9 C11 c3 M 6 4 3 1.530 109.458 -49.780 0.16326
10 H41 h1 E 9 6 4 1.090 109.461 -59.944 0.07659
11 H42 h1 E 9 6 4 1.090 109.498 179.984 0.01218
12 N10 n3 M 9 6 4 1.469 109.460 59.997 -0.81843
13 H40 hn E 12 9 6 1.009 106.738 66.225 0.35528
14 C9 c3 M 12 9 6 1.469 106.706 -179.987 0.15599
15 H38 h1 E 14 12 9 1.090 109.468 60.031 0.06718
16 H39 h1 E 14 12 9 1.090 109.483 -60.003 0.01172
17 C8 c3 M 14 12 9 1.530 109.478 179.970 0.19152
18 H36 h1 E 17 14 12 1.090 109.486 59.966 0.02452
19 H37 h1 E 17 14 12 1.090 109.484 -59.974 0.06755
20 N7 nh M 17 14 12 1.465 109.487 -179.998 -0.74364
21 H35 hn E 20 17 14 0.970 119.965 -0.011 0.43246
22 C6 ca M 20 17 14 1.387 119.990 -179.996 0.18283
23 C1 ca M 22 20 17 1.397 120.151 -5.650 -0.13917
24 H33 ha E 23 22 20 1.080 119.707 0.182 0.14465
25 C2 ca M 23 22 20 1.375 120.559 179.922 -0.13670
26 H34 ha E 25 23 22 1.080 119.691 179.939 0.14372
27 C3 ca M 25 23 22 1.397 120.538 0.016 0.17810
28 N26 nh B 27 25 23 1.388 120.121 179.979 -0.74116
29 C27 c3 3 28 27 25 1.465 119.988 6.756 0.18803
30 C28 c3 3 29 28 27 1.530 109.486 179.989 0.15381
31 N29 n3 B 30 29 28 1.469 109.441 -179.959 -0.81651
32 C30 c3 3 31 30 29 1.469 106.669 -179.952 0.16277
33 C31 c3 3 32 31 30 1.531 109.490 179.981 0.13210
34 O32 oh S 33 32 31 1.429 109.420 59.955 -0.58928
35 H60 ho E 34 33 32 0.968 106.759 179.985 0.39825
36 H58 h1 E 33 32 31 1.089 109.462 179.958 0.02449
37 H59 h1 E 33 32 31 1.090 109.446 -60.004 0.02275
38 H56 h1 E 32 31 30 1.091 109.454 -60.066 0.07622
39 H57 h1 E 32 31 30 1.090 109.538 59.938 0.01258
40 H55 hn E 31 30 29 1.009 106.678 -66.268 0.35517
41 H53 h1 E 30 29 28 1.089 109.471 -59.997 0.06029
42 H54 h1 E 30 29 28 1.089 109.452 60.030 0.02006
43 H51 h1 E 29 28 27 1.090 109.472 -59.942 0.04577
44 H52 h1 E 29 28 27 1.091 109.440 59.976 0.04687
45 H50 hn E 28 27 25 0.970 120.047 -173.252 0.43167
46 C4 ca M 27 25 23 1.398 119.823 0.012 -0.16746
47 C5 ca M 46 27 25 1.412 119.601 -0.046 -0.17117
48 C14 c M 47 46 27 1.474 119.639 179.936 0.61545
49 O15 o E 48 47 46 1.216 120.373 166.292 -0.58494
50 C16 ca M 48 47 46 1.475 119.193 -13.665 -0.19032
51 C17 ca M 50 48 47 1.395 120.598 -166.249 0.15808
52 O25 oh S 51 50 48 1.357 120.089 -0.044 -0.49918
53 H49 ho E 52 51 50 0.966 106.799 90.021 0.45155
54 C18 ca M 51 50 48 1.394 119.791 179.969 -0.11448
55 H46 ha E 54 51 50 1.080 119.752 -179.996 0.16132
56 C19 ca M 54 51 50 1.377 120.498 0.033 -0.11442
57 H47 ha E 56 54 51 1.080 119.755 179.976 0.16124
58 C20 ca M 56 54 51 1.394 120.550 -0.075 0.15780
59 O24 oh S 58 56 54 1.356 120.085 179.965 -0.49963
60 H48 ho E 59 58 56 0.967 106.774 90.082 0.45177
61 C21 ca M 58 56 54 1.395 119.748 0.079 -0.19013
62 C22 c M 61 58 56 1.475 120.615 -179.956 0.61472
63 O23 o M 62 61 58 1.217 120.406 -13.709 -0.58294
LOOP
C5 C6
C22 C4
C21 C16
IMPROPER
C8 C6 N7 H35
C1 C5 C6 N7
C6 C2 C1 H33
C1 C3 C2 H34
C2 C4 C3 N26
C27 C3 N26 H50
C22 C3 C4 C5
C14 C6 C5 C4
C5 C16 C14 O15
C14 C17 C16 C21
C16 C18 C17 O25
C17 C19 C18 H46
C18 C20 C19 H47
C19 C21 C20 O24
C22 C16 C21 C20
C4 C21 C22 O23
DONE
STOP
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Apr 11 2007 - 06:07:35 PDT
