AMBER Archive (2008)

Subject: Re: Re: AMBER: AdoMet parameterization with antechamber

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Mon Nov 24 2008 - 10:19:41 CST

Thanks so much for your instruction, David.

When running antechamber with all hydrogens, something strage was observed in the output. As in AdoMet, the sulfur atom is a sulfonium resulting in a system with 1 net positive charge. But the output message showed that the net charge was zero...
--------------
[c0225 sam]$ antechamber -i sam.pdb -fi pdb -o sam.prepin -fo prepi -c bcc -s 2
....
Info: Bond types are assigned for valence state 18 with penalty of 2

Running: /home/mjyang/amber9/amber9_mpi/exe/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

Total number of electrons: 210; net charge: 0

Running: $AMBERHOME/exe/divcon
....
-------------------------

I checked the prepi file produced by antechamber and found the line with SD atom:
----------------------
  19 SD s4 M 16 13 7 1.872 103.767 -61.554 -1.25307
----------------------

I don't know whether the running is right or not.
Any suggestion is greatly appreciated.

Thanks in advance.
Have a nice day.

-------
Jeffrey

In order to reproduce the running, the coordinates of SAM with all hydrogen atoms were copied and pasted as follows:
-------------
ATOM 1 N SAM 1 63.397 36.105 22.702 1.00 12.40
ATOM 2 HT1 SAM 1 62.405 35.824 22.841 1.00 0.00
ATOM 3 HT2 SAM 1 63.446 37.129 22.529 1.00 0.00
ATOM 4 HT3 SAM 1 63.946 35.871 23.554 1.00 0.00
ATOM 5 CA SAM 1 63.953 35.386 21.549 1.00 14.86
ATOM 6 HA SAM 1 63.370 35.643 20.677 1.00 0.00
ATOM 7 CB SAM 1 65.461 35.808 21.359 1.00 14.11
ATOM 8 HB1 SAM 1 65.917 35.028 20.718 1.00 0.00
ATOM 9 HB2 SAM 1 65.918 35.767 22.367 1.00 0.00
ATOM 10 CG SAM 1 65.897 37.177 20.745 1.00 15.20
ATOM 11 HG1 SAM 1 67.004 37.269 20.733 1.00 0.00
ATOM 12 HG2 SAM 1 65.485 38.023 21.335 1.00 0.00
ATOM 13 SD SAM 1 65.189 37.134 19.013 1.00 16.71
ATOM 14 CE SAM 1 66.605 37.841 18.157 1.00 19.15
ATOM 15 HE1 SAM 1 67.514 37.217 18.297 1.00 0.00
ATOM 16 HE2 SAM 1 66.822 38.857 18.549 1.00 0.00
ATOM 17 HE3 SAM 1 66.400 37.909 17.067 1.00 0.00
ATOM 18 C SAM 1 63.816 33.853 21.586 1.00 15.82
ATOM 19 OT1 SAM 1 64.265 33.167 20.651 1.00 18.70
ATOM 20 OT2 SAM 1 63.259 33.282 22.534 1.00 16.54
ATOM 21 C5' SAM 1 63.874 38.417 18.664 1.00 16.93
ATOM 22 H5' SAM 1 64.235 39.321 19.154 1.00 16.93
ATOM 23 H5'' SAM 1 63.815 38.447 17.555 1.00 0.00
ATOM 24 C4' SAM 1 62.514 38.192 19.241 1.00 18.89
ATOM 25 H4' SAM 1 62.127 37.204 18.913 1.00 0.00
ATOM 26 O4' SAM 1 62.529 38.196 20.691 1.00 15.15
ATOM 27 C1' SAM 1 61.431 38.979 21.237 1.00 18.44
ATOM 28 H1' SAM 1 60.874 38.387 21.992 1.00 0.00
ATOM 29 N9 SAM 1 62.187 40.106 21.832 1.00 18.09
ATOM 30 C5 SAM 1 62.277 41.912 23.224 1.00 17.88
ATOM 31 N7 SAM 1 63.540 41.800 22.660 1.00 17.18
ATOM 32 C8 SAM 1 63.450 40.761 21.873 1.00 17.14
ATOM 33 H8 SAM 1 64.280 40.394 21.270 1.00 0.00
ATOM 34 N1 SAM 1 60.322 42.681 24.566 1.00 19.08
ATOM 35 C2 SAM 1 59.582 41.648 24.022 1.00 20.03
ATOM 36 H2 SAM 1 58.546 41.572 24.347 1.00 0.00
ATOM 37 N3 SAM 1 60.010 40.704 23.115 1.00 18.16
ATOM 38 C4 SAM 1 61.410 40.895 22.744 1.00 17.70
ATOM 39 C6 SAM 1 61.684 42.847 24.190 1.00 19.48
ATOM 40 N6 SAM 1 62.362 43.862 24.743 1.00 17.52
ATOM 41 H61 SAM 1 63.322 44.033 24.519 1.00 0.00
ATOM 42 H62 SAM 1 61.931 44.483 25.398 1.00 0.00
ATOM 43 C2' SAM 1 60.344 38.752 20.132 1.00 20.60
ATOM 44 H2'' SAM 1 59.522 39.381 20.499 1.00 0.00
ATOM 45 O2' SAM 1 59.648 37.724 19.551 1.00 24.88
ATOM 46 H2' SAM 1 59.580 37.887 18.607 1.00 0.00
ATOM 47 C3' SAM 1 61.368 39.163 18.990 1.00 21.43
ATOM 48 H3' SAM 1 61.715 40.211 19.102 1.00 0.00
ATOM 49 O3' SAM 1 61.142 39.227 17.614 1.00 24.71
TER
END
-------------------

>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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