AMBER Archive (2006)

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

From: Junmei Wang (jwang_at_encysive.com)
Date: Tue Nov 28 2006 - 15:54:42 CST

If you would like to send me your molecule, I will try my best to figure out what's the problem. Clearly, some atom types could not be recognized properly. It may be because of the improper atom names.

All the best

Junmei

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of daaldamo_at_hotmail.com
Sent: Monday, November 27, 2006 9:30 PM
To: amber_at_scripps.edu
Subject: AMBER: Problem about dummy atoms when running antechamber

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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