AMBER Archive (2009)

Subject: Re: [AMBER] Antechamber problem

From: David A. Case (
Date: Fri Mar 27 2009 - 07:29:48 CDT

On Fri, Mar 27, 2009, 欧阳德方 wrote:
> When I run antechamber of AMBER9 to deal with my pdb file, there is one problem. I attached my pdb file. The command:
> antechamber -nc 4 -i 4+arginine.pdb -fi pdb -o 4+arginine.prepin -fo prepi -c bcc

All atom names in a given residue must be unique, but you have lots of
atoms named "H" and "C", etc. My guess is that you need to fix this
problem; although antehcamber is supposed to fix it for you, there may be
an error there.

If you set "-j 5" on the antechamber line, the calculation will proceed
further, but mopac complains about an odd number of electrons with a
charge of +4. The structure looks OK to me, but it is big enough that I
could be missing a problem. Check the structure around atom 33; if that
doesn't help, try breaking the molecule into smaller pieces until you
can localize the error.

...good luck...dac

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