AMBER: problem of calculate the charge2

From: ping jiang <>
Date: Tue, 27 Dec 2005 18:17:05 -0800 (PST)

Dear Amber Users,

I forgot to ask in my previous email. Is it possible
to use antechamber to calculate undecyl {CH3(CH2)10CO}
with 0 net charge? If I put H with O atom
{CH3(CH2)10COH}, with antechamber (-c bcc -nc -1), it
works. But without H atom, it doesn't work, I want
this system has 0 net charge, so that it can be used
to connect other amino acid groups.

$AMBERHOME/exe/antechamber -i undecyl.pdb -fi pdb -o
undecyl.prepin -fo prepi -c bcc -s 2 -nc -j 4

it shows:

Cannot successfully assign bond type for this
molecule, please:
(1) double check the structure (the connectivity)
(2) adjust atom valence penalty parameters in APS.DAT,
(3) increase MAXVASTATE in define.h and recompile

Running: /a1/a1/home/jiang/amber/amber8/exe/atomtype

Total number of electrons: 95; net charge:0
Number of electrons is odd: 95
Please check the total charge and your -nc flag

How to change the valence penalty parameters for this
molecule {CH3(CH2)10CO}? Let the programe can
recognize the atom type and charge.
Here I also attached the PDB file for this molecule.
Thank you very much,

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Received on Wed Jan 04 2006 - 18:17:00 PST
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