On Sun, Nov 23, 2008, Jeffrey wrote:
> Running: /home/mjyang/amber9/amber9_mpi/exe/bondtype -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full
>
>
> The content in sama.pdb file is as follows:
> ----------
> ATOM 1836 N SAM 402 63.397 36.105 22.702 1.00 12.40 N
> ATOM 1837 CA SAM 402 63.953 35.386 21.549 1.00 14.86 C
> ATOM 1838 C SAM 402 63.816 33.853 21.586 1.00 15.82 C
> ATOM 1839 O SAM 402 63.259 33.282 22.534 1.00 16.54 O
> ATOM 1840 OXT SAM 402 64.265 33.167 20.651 1.00 18.70 O
> ATOM 1841 CB SAM 402 65.461 35.808 21.359 1.00 14.11 C
> ATOM 1842 CG SAM 402 65.897 37.177 20.745 1.00 15.20 C
> ATOM 1843 SD SAM 402 65.189 37.134 19.013 1.00 16.71 S
> ATOM 1844 CE SAM 402 66.605 37.841 18.157 1.00 19.15 C
> ATOM 1845 C5' SAM 402 63.874 38.417 18.664 1.00 16.93 C
> ATOM 1846 C4' SAM 402 62.514 38.192 19.241 1.00 18.89 C
> ATOM 1847 O4' SAM 402 62.529 38.196 20.691 1.00 15.15 O
> ATOM 1848 C3' SAM 402 61.368 39.163 18.990 1.00 21.43 C
> ATOM 1849 O3' SAM 402 61.142 39.227 17.614 1.00 24.71 O
> ATOM 1850 C2' SAM 402 60.344 38.752 20.132 1.00 20.60 C
> ATOM 1851 O2' SAM 402 59.648 37.724 19.551 1.00 24.88 O
> ATOM 1852 C1' SAM 402 61.431 38.979 21.237 1.00 18.44 C
> ATOM 1853 N9 SAM 402 62.187 40.106 21.832 1.00 18.09 N
> ATOM 1854 C8 SAM 402 63.450 40.761 21.873 1.00 17.14 C
> ATOM 1855 N7 SAM 402 63.540 41.800 22.660 1.00 17.18 N
> ATOM 1856 C5 SAM 402 62.277 41.912 23.224 1.00 17.88 C
> ATOM 1857 C6 SAM 402 61.684 42.847 24.190 1.00 19.48 C
> ATOM 1858 N6 SAM 402 62.362 43.862 24.743 1.00 17.52 N
> ATOM 1859 N1 SAM 402 60.322 42.681 24.566 1.00 19.08 N
> ATOM 1860 C2 SAM 402 59.582 41.648 24.022 1.00 20.03 C
> ATOM 1861 N3 SAM 402 60.010 40.704 23.115 1.00 18.16 N
> ATOM 1862 C4 SAM 402 61.410 40.895 22.744 1.00 17.70 C
> END
Antechamber needs as input a pdb file with all hydrogens added. sleap has an
"hbuild" routine which should do this (I've not used it myself), and many
other programs can also do this.
...dac
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Received on Fri Dec 05 2008 - 16:29:20 PST
