Hi, Avneet,
Antechamber cannot handle open valence molecules, this is why you got
some error message. We provided some examples of generating peptoid
residues in the antechamber homepage. Here is the link:
http://amber.scripps.edu/antechamber/example.html
All the best
Junmei
Dear All
I have valine residue as a peptoid (sidechain appended to amide nitrogen
instead of alpha carbon) and i want to load it as N-terminal residue,
C-terminal residue and a simple residue.
I prepared three files for them Nnval, Cnval and nval respectively, in
accordance with the view provided for such molecules in leap.
Then i give the command to load the pdb files of these three using
antechamber. the command and the comments received in the terminal are
as follows:
$AMBERHOME/exe/antechamber -i Nnval.pdb -fi pdb -o Nnval.prepin -fo
prepi -c bcc -s 2
Running: /usr/local/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/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 56; net charge: 0
Running: /usr/local/amber8/exe/divcon
Running: /usr/local/amber8/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p
/usr/local/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/amber8/exe/atomtype -i ANTECHAMBER_PREP.AC0 -o
ANTECHAMBER_PREP.AC -p gaff
Running: /usr/local/amber8/exe/prepgen -i ANTECHAMBER_PREP.AC -f int -o
Nnval.prepin -rn "Nva " -rf molecule.res
[root.res exe]# $AMBERHOME/exe/antechamber -i Cnval.pdb -fi pdb -o
Cnval.prepin -fo prepi -c bcc -s 2
Running: /usr/local/amber8/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC -o
ANTECHAMBER_BOND_TYPE.AC -f ac -j full
Bond types are assigned for valence state 4 with penalty of 4
Running: /usr/local/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 62; net charge: 0
Running: /usr/local/amber8/exe/divcon
Running: /usr/local/amber8/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p
/usr/local/amber8/dat/antechamber/BCCPARM.DAT -j 4
Bond types are assigned for valence state 4 with penalty of 4
Running: /usr/local/amber8/exe/atomtype -i ANTECHAMBER_PREP.AC0 -o
ANTECHAMBER_PREP.AC -p gaff
Running: /usr/local/amber8/exe/prepgen -i ANTECHAMBER_PREP.AC -f int -o
Cnval.prepin -rn "Nva " -rf molecule.res
[root.res exe]# $AMBERHOME/exe/antechamber -i nval.pdb -fi pdb -o
nval.prepin -fo prepi -c bcc -s 2
Running: /usr/local/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/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 54; net charge: 0
Running: /usr/local/amber8/exe/divcon
Running: /usr/local/amber8/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p
/usr/local/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/amber8/exe/atomtype -i ANTECHAMBER_PREP.AC0 -o
ANTECHAMBER_PREP.AC -p gaff
Running: /usr/local/amber8/exe/prepgen -i ANTECHAMBER_PREP.AC -f int -o
nval.prepin -rn "Nva " -rf molecule.res
I am also attaching the pdb files and the prepin files that were made
Please suggest how to proceed
Regards
Avneet Saini
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Received on Sun Oct 22 2006 - 06:07:07 PDT
