AMBER Archive (2009)

Subject: Re: [AMBER] antechamber problems

From: Nicholas Musolino (musolino_at_MIT.EDU)
Date: Thu Apr 09 2009 - 13:03:45 CDT

I think that antechamber is interpreting the 34.18, 34.92, and other
numbers in column 8 as partial charges on the respective atoms. Those
numbers add up to 349, which is the net charge antechamber is assuming.

I would suggest trying (i) manually changing those numbers in the mol2
file, (ii) using the "-nc 0" option to indicate a net charge of zero,
or (iii) both.

On Apr 9, 2009, at 1:12 PM, Jia Xu wrote:

> Dear amber users,
> I tried to simulate an organic compound (structure file is
> attached)
> using antechamber and GAFF according to the tutorial 5 (
> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_five/).
> However, when tried to creat the "prepin" file, I failed to obtain
> it.
> The command used is $AMBERHOME/exe/antechamber -i m1.mol2 -fi mol2 -o
> m1.prepin –fo prepi –c bcc –s 2
> The screen output is shown as follows.
> Running: /usr/local/dock6/bin/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o
> ANTECHAMBER_BOND_TYPE.AC -f ac -j full
>
> Running: /usr/local/dock6/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
>
> Total number of electrons: -213; net charge: 349
> Number of electrons is odd: -213
> Please check the total charge and your -nc flag
>
> Can anyone help me to solve this problem?
> Thanks in advance!
>
> --
> Jia Xu
> <m1.mol2>_______________________________________________
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