Thnks alot Benjamin, it worked, i smply set the envrnment andf it wrkd.
Thnks alot
I really thnkful to u.
Anju
On 4/10/07, Benjamin Juhl <itbbju.itb.uni-stuttgart.de> wrote:
>
> 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
>
>
--
Anju Sharma
Project Fellow,
NIT, Hamirpur (H.P.)
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Received on Wed Apr 11 2007 - 06:07:41 PDT
