AMBER Archive (2006)

Subject: AMBER: Problem loading peptoid residues with antechamber

From: nur avneet (nuravneet_at_yahoo.co.in)
Date: Wed Oct 18 2006 - 01:23:42 CDT

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_at_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_at_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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