AMBER Archive (2009)

Subject: RE: [AMBER] problem with energy calculations

From: Lake, Thomas (thomas.lake08_at_imperial.ac.uk)
Date: Sun Jul 12 2009 - 08:35:33 CDT

I removed the periodic box from the trajectory file (by specifying 'nobox' in ptraj).

However I still got this error message.

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf Of Carlos Simmerling
Sent: 10 July 2009 18:26
To: AMBER Mailing List
Subject: Re: [AMBER] problem with energy calculations

why are you getting virtual box energies in the gas phase? is the system
really periodic?

On Fri, Jul 10, 2009 at 12:13 PM, Thomas Lake
<thomas.lake08_at_imperial.ac.uk>wrote:

> Hello,
>
> I have been modelling a peptide and am trying to carry out energy
> calculations of it in the gas-phase. For this I use the mm_pbsa script,
> but using only MM.
>
> I am able to calculate the energy of just the peptide. However when I
> include counterions (but no solvent), I get an error message:
>
> 'The system has extended beyond the extent of virtual box'
>
> If I do reimaging of the trajectory (image center familiar) then I dont
> get this error message. However the energies that are calculated give
> very high vdW energies for certain frames. This I think is because
> counterions have come into close contact in these frames.
>
> I cannot think of any more possible solutions for this, so wandering if
> anyone help me.
>
> Regards
>
> Thomas Lake
> Imperial College London
>
>
>
>
>
>
>
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