Hi,
If you would like send me your molecule, probably I can help you figure
out what's going on.
All the best
Junmei
Dear Amber users
I ran antechamber to parameterize my molecule consists of 354
atoms.
It is the organic molecule which has long aliphatic branches at
one side and molecular
rod with successional phenyl rings.
Next was my antechamber command...
------------------------------------------------------------------------
------
./antechamber -i nano.mol2 -fi mol2 -o nano.prepin -fo prepi -c
bcc -s 2 -nc 0 -j 5 -rn DUM
------------------------------------------------------------------------
------
after processing, i could get some messages and nano.prepin
file.
messages from antechamber processing was..
------------------------------------------------------------------------
------
Running: /usr/local/amber8/antechamber-1.27//exe/bondtype -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j part
Info: the atom number exceeds the MAXATOM, reallocate memory
automatically
Running: /usr/local/amber8/antechamber-1.27//exe/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Info: the atom number exceeds the MAXATOM, reallocate memory
automatically
Total number of electrons: 1188; net charge: 0
Running: $AMBERHOME/exe/divcon
Running: /usr/local/amber8/antechamber-1.27//exe/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/usr/local/amber8/antechamber-1.27//dat/antechamber/BCCPARM.DAT -s 2 -j
1
Running: /usr/local/amber8/antechamber-1.27//exe/atomtype -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
Info: the atom number exceeds the MAXATOM, reallocate memory
automatically
Unrecognized atomic name DU58, exit
Unrecognized atomic name DU59, exit
Unrecognized atomic name DU04, exit
Unrecognized atomic name DU47, exit
Unrecognized atomic name DU48, exit
Unrecognized atomic name DU53, exit
Info: the atom number exceeds the MAXATOM, reallocate memory
automatically
Unrecognized atomic name DU58, exit
Unrecognized atomic name DU59, exit
Unrecognized atomic name DU04, exit
Unrecognized atomic name DU47, exit
Unrecognized atomic name DU48, exit
Unrecognized atomic name DU53, exit
Running: /usr/local/amber8/antechamber-1.27//exe/atomtype -i
ANTECHAMBER_PREP.AC0 -o ANTECHAMBER_PREP.AC -p gaff
Info: the atom number exceeds the MAXATOM, reallocate memory
automatically
Unrecognized atomic name DU58, exit
Unrecognized atomic name DU59, exit
Unrecognized atomic name DU04, exit
Unrecognized atomic name DU47, exit
Unrecognized atomic name DU48, exit
Unrecognized atomic name DU53, exit
Running: /usr/local/amber8/antechamber-1.27//exe/prepgen -i
ANTECHAMBER_PREP.AC -f int -o nano.prepin -rn "DUM" -rf molecule.res
Info: the atom number exceeds the MAXATOM, reallocate memory
automatically
Unrecognized atomic name DU58, exit
Unrecognized atomic name DU59, exit
Unrecognized atomic name DU04, exit
Unrecognized atomic name DU47, exit
Unrecognized atomic name DU48, exit
Unrecognized atomic name DU53, exit
The atom number exceeds the MAXATOM, reallocate memory
------------------------------------------------------------------------
------
as you see, in nano.prepin file, there were six unrecognized
atomic names
I thought that they are dummy atoms which might be treated
manually.
but i don't know which atom is correct instead of dummy
and Xleap can't load nano.prepin because of dummy atoms.
Question 1. It's possible to treat dummy atoms manually? then
how?
Question 2. Can the antechamber parameterize the unusually long
organic molecule
like mine?
Please tell me....T.T
Thanks
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Dec 08 2006 - 16:23:17 PST
