My apologies for the below email. It turns out that I got my prmtop's
confused - I was doing some testing and had to switch to a different machine
in the mean time...
So, CHAMBER gave me the right prmtop after all.
Also, in case anyone is interested, by comparison with other prmtop's, I
noticed that IFBOX setting is the number in the 3rd row, 8th column of
the %FLAG POINTERS %FORMAT(10I8) part of the prmtop file. This, together
with all other specifications, of course I could have found here:
http://ambermd.org/formats.html
Apologies again,
Marc
On 7 April 2011 08:53, Marc van der Kamp <marcvanderkamp.gmail.com> wrote:
> Hi all,
>
> I am trying to run with the CHARMM (22/27) force-field in AMBER
> (sander/pmemd). My system is a protein in a box of water. After obtaining
> the prmtop and inpcrd from the CHARMM psf/crd(/prm/top) - using the -box
> option to get the box information in the inpcrd, I can run a minimization
> (of solvent) successfully.
> However, when I want to run a brief MD simulation of the solvent
> afterwards, I get the following error:
>
> (NTB /= 0 && NTP /= 0) but IFBOX == 0
> This combination is not supported
>
> I have used the exact same input before using a 'normal' (leap-generated)
> AMBER prmtop/inpcrd.
> From earlier posts, I understand that IFBOX is set in the prmtop, and means
> that there is no periodic box?
> So, my question is two-fold:
> 1) Where can I change the IFBOX in the prmtop (manually)
> 2) How can I get CHAMBER to do this correctly, i.e. put IFBOX == 1 (I
> presume) when I give it the -box <x-length> <y-length> <z-length> option?
>
> Many thanks,
> Marc
>
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Received on Thu Apr 07 2011 - 02:00:03 PDT
