Without removing the hydrogen from amine, I got error message of odd electrons from antechamber. I removed it because the hydrogen cant form bonding with the sp2 hybridized nitrogen
________________________________
From: case <case.biomaps.rutgers.edu>
To: jun kit <klorin2002.yahoo.co.uk>
Sent: Thursday, 24 November 2011, 23:29
Subject: Re: [AMBER] help with antechamber
On Thu, Nov 24, 2011, jun kit wrote:
> Thanks David for your assistance. Now I came to last step which error
> occur when using tleap to saveamberparams
>
> Atom XXX does not have a type.
Usually, looking at what "XXX" is, and *all* the surrounding messages gives
a good clue to what is going on.
>
> 1. I determined the charges of "amine" and "phenol" by removing a
> hydrogen in "amine" and add a hydrogen in "phenol"
I think you need to proceed much more slowly here. I doubt that you want to
remove a hydrogen from the amine, and the place you put the hydrogen on the
phenol is in the middle of a C-C bond. Learn how to use visualization
programs, and think about the overall charges and chemical bonding structures
of the molecules you are working with.
Next, try to do an amber simulation of just one of your molecules. Set up the
library and frcmod files, load them into LEaP, and run a minimization or sort
molecular dynamics simulation. Use the visualization program to look at the
results, and make sure you are confident about what you did.
Do the same for other components; then you should be able to constructing a
condensed-phase mixture for the two.
...good luck...dac
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Received on Thu Nov 24 2011 - 08:30:03 PST
