AMBER Archive (2006)

Subject: RE: AMBER: Problem about dummy atoms when running antechamber

From: Junmei Wang (jwang_at_encysive.com)
Date: Thu Dec 07 2006 - 11:14:58 CST

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

         

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