After I analyze my structure with MOE, I found out that it is not necessary to add a hydrogen at the "phenol"group. The "phenol" group and "amine" group is meant to form a hydrogen bond. So a O at "phenol" group will be O- and a N in the "amine" group will be N+. But now it raises some question:
1. Since these both molecules is bonded by hydrogen bond (indeed I need this H-bond for study), do I need to derive their charges seperately or derive them as a whole?
2. If I load the structure into antechamber or gaussian, how does the program know whether or not my O is negative and my N is positive? The -nc flag in antechamber will assign it correctly by automatic?
3. When I load the structure in to LEAP, do I still need to use TER card between this "phenol" and "amine" or in between "phenol-amine"?
I upload the residue for your reference
P/S: Sry i am asking too much qyuestion because I am a physics student and quite unfamiliar with bonding stuff
Thanks
min
________________________________
From: case <case.biomaps.rutgers.edu>
To: jun kit <klorin2002.yahoo.co.uk>
Sent: Thursday, 24 November 2011, 19:37
Subject: Re: [AMBER] help with antechamber
On Thu, Nov 24, 2011, jun kit
wrote:
> Without removing the hydrogen from amine, I got error message of odd
> electrons from antechamber.
Antechamber assumes that the net charge on the molecule is zero, unless you
add the "-nc" flag; so far a +1 charge you need to add "-nc 1". Similarly,
your "phenol" group probably has a charge of -2.
....dac
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Received on Sun Nov 27 2011 - 08:00:02 PST
