AMBER: AdoMet parameterization with antechamber

From: Jeffrey <jeffry20072008.yahoo.cn>
Date: Sun, 23 Nov 2008 23:55:30 +0800

Dear all,

    I am going to get the parameters of AdoMet cofactor in many methyltransferases. But when trying with antechamber, the program halted with the following message:
------------------
[c0225 sam]$ antechamber -i sama.pdb -fi pdb -o sam1.prepin -fo prepi -c bcc -s 2
Running: /home/mjyang/amber9/amber9_mpi/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full

Warning: the assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase MAXVASTATE in define.h and recompile bondtype.C
(4) increase PSCUTOFF in define.h and recompile bondtype.C
    Be cautious, use a large value of PSCUTOFF (>10) will significantly increase the computer time
Error: cannot run "/home/mjyang/amber9/amber9_mpi/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in judgebondtype() of antechamber.c properly, exit
---------

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
-------------

Could someone please tell me how to fix the problem and what's the intrinsic mechanism of the error?

Any suggestion is greatly appreciated.
Thanks so much for your time.

Have a nice day.
----
Jeffrey
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Received on Fri Dec 05 2008 - 16:28:01 PST
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