Re: [AMBER] Questions regarding AMBER

From: FyD <>
Date: Sun, 13 Oct 2013 16:05:20 +0200

Dear Kamali,

if you have an open valency in your molecular system and/or want to
generate a molecular fragment you might try R.E.D. Server at

regards, Francois

> Thank you very much, Dr. Case; I wasn't aware that the "-nc" flag was only
> for amb1-bcc calculations. Would you be able to tell me what the warning
> means? It seems to me that antechamber is misinterpreting the fact that the
> N1 atom now only has 2 bonds as an indication of incomplete valence, but
> I'm not sure how much this will distort the resulting charges, and also if
> there's a way to let antechamber know that the "incomplete valency" is
> intentional.

> On Sat, Oct 12, 2013 at 11:39 AM, David Case <> wrote:
>> > On Oct 12, 2013, at 10:22 AM, Kamali Sripathi <>
>> wrote:
>> >
>> >
>> > I am using Gaussian and antechamber to parameterize an N1-unprotonated
>> > guanine for RNA. I initially generated a prepc file while forgetting to
>> add
>> > the "-nc -1" flag. I re-ran the calculations using this flag, but the two
>> > resulting prepc files are the same. I have compared prepc files for other
>> > molecules with and without the "-nc" flag and found the same thing
>> happen.
>> The -nc flag only applies to am1-bcc charge calculations. You provided
>> the net charge to Gaussian in its inout file.
>> ...dac

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Received on Sun Oct 13 2013 - 07:30:03 PDT
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