On Wed, 2014-05-28 at 11:21 -0400, Lara rajam wrote:
> Dear Amber
>
> I am trying to run the NAMD with the amber force field
>
> I have generated the prmtop and the inpcrd with xleap and solvated the
> system with
> solvatebox TIP3P 12 A
>
> when i tried NAMD my protein comes out of the box and the water box got
> splited
>
> I fell the problem is owing to the cell basis vector 1 , 2 and 3 and the
> cellorigin could be wrong
>
> is the cell basis vector should be given as the last line of the inpcrd
> file as vector 1, 2 and 3
The last line of the inpcrd file is the lengths of the 3 cell vectors
(a, b, then c) followed by the angles (alpha, beta, then gamma). The
cell vectors (that NAMD uses) needs to be calculated from these lengths
and angles.
Have you visited this webpage yet:
http://ambermd.org/namd/namd_amber.html ? This shows you how to define
a truncated octahedron (or a rhombic dodecahedron).
> what about the cell origin , how one can find it in amber generated files
The "cell origin" keyword in NAMD has no analog in Amber. Fortunately,
the "cell origin" is arbitrary and has no impact on the simulation (just
on visualization). You can reimage afterwards, setting the origin to
wherever you want, with cpptraj.
> can anyone give me some useful links or give me some suggestions since i am
> trying it for the first time
On the Amber side, see the webpage I mentioned above. Googling "amber
in namd" brings up this page as well as others you may find helpful.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed May 28 2014 - 09:00:02 PDT
