AMBER Archive (2002)

Subject: Re: anal in AMBER7 gives inconsistent results with itself

From: Prabal Maiti (maiti_at_wag.caltech.edu)
Date: Mon Jul 08 2002 - 00:46:31 CDT

Thanks!

On Sat, 6 Jul 2002, David A. Case wrote:

> On Fri, Jul 05, 2002, Prabal Maiti wrote:
>
> > I was trying to get the energy for each of the residue in a 10-mer B-DNA.
> > I used 20A cutoff.
>
> Please try with no cutoff.

I tried to use a cutoff distance 999 assuming that is big enough to have
all non-bond pairs with no cutoff ( I guess thats what you also mean by no
cutoff). Still the same problem.

>
> Also, what are your groups? You seem to have 21 of them, which seems odd;
> is there any chance you have some atoms that are in more than one group?
> The groups have wildly different energies, which suggests that maybe the
> problem is in that direction.
>
In the system I have 10-mer DNA (20 bases), Na+ and water (all together
11638 atoms). So I have defined 20 bases as 20 groups and I guess rest of
the system is treated as one more group. Thats why we see 21 groups. I
have verified this by explicitly definfing the 21 st groups with the atoms
belonging to Na+ and water.

Prabal

> ..good luck...dac
>
> 

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Prabal K Maiti                             Email:maiti_at_wag.caltech.edu
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