I would appreciate receiving suggestions as to the most likely route
to get prmtop/inpcrd for carbon monoxide with antechamber.
........................
$AMBERHOME/exe/antechamber -i CO.pdb -fi pdb -o CO.mol2 -fo mol2 -c bcc -s 2
Running: /usr/local/amber10/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
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 PSCUTOFF in define.h and recompile bondtype.c
Be cautious, use a large value of PSCUTOFF (>100) will
significantly increase the computation time
Error: cannot run "/usr/local/amber10/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
judgebondtype() of antechamber.c properly, exit
.........................................
File atomtype.inf:
====================================================================================
-------------------------------ring property
(I)------------------------------------
====================================================================================
-------------------------------ring property
(II)------------------------------------
====================================================================================
-------------------------------ring property
(III)-----------------------------------
atom[ 1] (C ) is not in any ring (nr[1]=1)
atom[ 2] (O ) is not in any ring (nr[2]=1)
====================================================================================
-------------------------------aromatic
property------------------------------------
====================================================================================
-------------------------------electronic
property----------------------------------
atom [ 1] (C ) is not an electron-withdrew atom
atom [ 2] (O ) is an electron-withdrew atom
====================================================================================
--------------------------------connectivity
property-------------------------------
atom[ 1] (C ) 2 O
atom[ 2] (O ) 1 C
----------------------------------------END-----------------------------------------
Files antechamber_bond_type.ACO and .AC:
CHARGE 0.00 ( 0 )
Formula: C1 O1
ATOM 1 C CMO 155 16.534 26.761 4.984 0.000000 C
ATOM 2 O CMO 155 17.541 26.592 4.364 0.000000 O
BOND 1 1 2 0 C O
I was using amber10 with ambertools 1.2, standard APS.DAT
thanks
francesco pietra
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Received on Sat Feb 06 2010 - 03:00:02 PST
