AMBER Archive (2007)

Subject: Re: AMBER: Problem while using antechamber

From: Benjamin Juhl (itbbju_at_itb.uni-stuttgart.de)
Date: Tue Apr 10 2007 - 02:12:13 CDT

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_at_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

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