AMBER Archive (2009)
Subject: Re: [AMBER] antechamber problems
From: Jia Xu (xujia.ruc_at_gmail.com)
Date: Fri Apr 10 2009 - 09:41:53 CDT
Thanks for the suggestions given by you two, they are very helpful.
On Fri, Apr 10, 2009 at 2:03 AM, Nicholas Musolino <musolino_at_mit.edu> wrote:
> 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 (
>> 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
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