Hi,
I checked the structure of 6tna.pdb and found 2MG is a "standard"
residue that connect to and is connected to other residues. Unlike the
standalone organic molecules, you need to run antechamber step by step
to generate the residue topology file for 2MG. Details is presented in
the antechamber homepage.
http://amber.scripps.edu/antechamber/antechamber.html .
Best
Junmei
==================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals Inc.
7000 Fannin, Houston TX 77030
Tel: 713-578-6649
Email: jwang.encysive.com
http://amber.scripps.edu/antechamber/antechamber.html
==================================================
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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Received on Fri Sep 02 2005 - 21:53:01 PDT
