AMBER Archive (2005)

Subject: AMBER: Antechamber error "Cannot successfully assign bond type for this molecule"

From: Whitney Allen (whitneygallen_at_yahoo.com)
Date: Thu Aug 25 2005 - 11:13:11 CDT

Hi,
I am trying to run antechamber to get parameters for the modified residues found in TRNA (6tna.pdb). Listed below are the commands I gave and the corresponding error message. I seem to get output files, but because of this error message I am not sure if they are correct and if I should be doing something else. Second, if I get the parameters for the modified residues can I use them for other structures if the modified residue has the same atoms (basically a slightly modified version of the 6tna.pdb structure)?
Thanks for the help
Whitney
 
 $AMBERHOME/exe/antechamber -i resi10.pdb -fi pdb -o resi10.prepin -fo prepi -c bcc -s 2

Running: /usr/local/fbscapp/amber8/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full
Cannot successfully assign bond type for this molecule, 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
Running: /usr/local/fbscapp/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 172; net charge: 0
Running: /usr/local/fbscapp/amber8/exe/divcon
Running: /usr/local/fbscapp/amber8/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/local/fbscapp/amber8/dat/antechamber/BCCPARM.DAT -j 4
Cannot successfully assign bond type for this molecule, 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

Running: /usr/local/fbscapp/amber8/exe/atomtype -i ANTECHAMBER_PREP.AC0 -o ANTECHAMBER_PREP.AC -p gaff

Running: /usr/local/fbscapp/amber8/exe/prepgen -i ANTECHAMBER_PREP.AC -f int -o resi10.prepin -rn "2MG " -rf molecule.res

 

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