AMBER Archive (2006)

Subject: RE: AMBER: Problem loading peptoid residues with antechamber

From: nur avneet (nuravneet_at_yahoo.co.in)
Date: Wed Oct 18 2006 - 23:05:15 CDT

We have very limited facilities and donot have Sybyl.
 
 Please suggest the relevant way so that i may proceed.

Junmei Wang <jwang_at_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_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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