>this is my pdb file
>HEADER PROTEIN
>COMPND jmins0.pdb
>AUTHOR GENERATED BY BABEL 1.3
>HETATM 1 N1 RET 1 0.000 0.000 0.000 1.00 0.00
>HETATM 2 C2 RET 1 1.429 0.000 0.000 1.00 0.00
>HETATM 3 C3 RET 1 -0.727 1.095 0.000 1.00 0.00
>HETATM 4 C4 RET 1 -2.140 1.127 0.000 1.00 0.00
>HETATM 5 C5 RET 1 -2.895 2.273 0.000 1.00 0.00
>HETATM 6 C6 RET 1 -4.315 2.170 0.000 1.00 0.00
>HETATM 7 C7 RET 1 -2.277 3.607 -0.000 1.00 0.00
>HETATM 8 C8 RET 1 -5.201 3.205 0.000 1.00 0.00
>HETATM 9 C9 RET 1 -6.609 3.033 -0.000 1.00 0.00
>HETATM 10 C10 RET 1 -7.524 4.040 -0.000 1.00 0.00
>HETATM 11 C11 RET 1 -8.933 3.721 -0.000 1.00 0.00
>HETATM 12 C12 RET 1 -7.123 5.452 -0.000 1.00 0.00
>HETATM 13 C13 RET 1 -9.934 4.602 -0.000 1.00 0.00
>HETATM 14 H14 RET 1 1.912 1.000 0.000 1.00 0.00
>HETATM 15 H15 RET 1 1.896 -0.505 0.871 1.00 0.00
>HETATM 16 H16 RET 1 1.896 -0.505 -0.871 1.00 0.00
>HETATM 17 H17 RET 1 -0.417 -0.878 0.000 1.00 0.00
>HETATM 18 H18 RET 1 -0.263 2.100 0.000 1.00 0.00
>HETATM 19 H19 RET 1 -2.673 0.167 0.000 1.00 0.00
>HETATM 20 H20 RET 1 -4.731 1.154 -0.000 1.00 0.00
>HETATM 21 H21 RET 1 -2.572 4.197 -0.880 1.00 0.00
>HETATM 22 H22 RET 1 -2.571 4.197 0.880 1.00 0.00
>HETATM 23 H23 RET 1 -1.175 3.598 -0.000 1.00 0.00
>HETATM 24 H24 RET 1 -4.841 4.246 0.000 1.00 0.00
>HETATM 25 H25 RET 1 -6.970 1.996 -0.000 1.00 0.00
>HETATM 26 H26 RET 1 -9.179 2.651 -0.000 1.00 0.00
>HETATM 27 H27 RET 1 -7.504 5.990 -0.880 1.00 0.00
>HETATM 28 H28 RET 1 -7.504 5.990 0.880 1.00 0.00
>HETATM 29 H29 RET 1 -6.030 5.600 -0.000 1.00 0.00
>HETATM 30 H30 RET 1 -10.981 4.318 -0.000 1.00 0.00
>HETATM 31 H31 RET 1 -9.805 5.680 -0.000 1.00 0.00
>CONECT 1 2 3 17
>CONECT 2 1 14 15 16
>CONECT 3 1 4 18
>CONECT 4 3 5 19
>CONECT 5 4 6 7
>CONECT 6 5 8 20
>CONECT 7 5 21 22 23
>CONECT 8 6 9 24
>CONECT 9 8 10 25
>CONECT 10 9 11 12
>CONECT 11 10 13 26
>CONECT 12 10 27 28 29
>CONECT 13 11 30 31
>CONECT 14 2
>CONECT 15 2
>CONECT 16 2
>CONECT 17 1
>CONECT 18 3
>CONECT 19 4
>CONECT 20 6
>CONECT 21 7
>CONECT 22 7
>CONECT 23 7
>CONECT 24 8
>CONECT 25 9
>CONECT 26 11
>CONECT 27 12
>CONECT 28 12
>CONECT 29 12
>CONECT 30 13
>CONECT 31 13
>MASTER 0 0 0 0 0 0 0 0 31 0 31 0
>END
>
>and i run ../exe/antechamber -nc 1 -i jmins0.pdb -fi pdb -o jmins0.prep
>-fo prepi -c -bcc
>it woked fine until parmchk
>../exe/parmchk -i jmins0.prep -f prepi -o frcmod
>then it turned Segmentation fault
>
>Thanks,
>Chutintorn
>
>
David A. Case wrote:
>On Mon, May 24, 2004, Chutintorn Punwong wrote:
>
>
>
>>I've run the antechamber test case (tp.pdb) it worked fine.
>>
>>
>>
>>>When I run parmchk command to build frcmod file, it always give
>>>
>>>
>>segmentation fault.
>>
>>
>
>Since it works for the test cases, but not for your files, we would need
>to know more about your input files, and exactly what arguments you used.
>
>...regards...dac
>
>
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Received on Thu May 27 2004 - 19:53:00 PDT
