We have very limited facilities and donot have Sybyl.
Please suggest the relevant way so that i may proceed.
Junmei Wang <jwang.encysive.com> wrote:Message 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 - 06:07:12 PDT
