Thanks Dan and Dac!
.Dan: I checked the prmtop file specification (
http://ambermd.org/formats.html) for BOX_DIMENSIONS and it says:
OLDBETA : periodic box, angle between the XY and YZ planes in
degrees.
*This is now redundant, as it is present in the
inpcrd files. It is ignored here.*
Does it mean that even if I dont change these values in prmtop file then
also it is fine because I have modified the last line of restart file from :
90.0 to 109.4712190?
.Dac: My restart file is netcdf formatted so I can not visualize it using
vi editor. As an alternate, I generated the inpcrd file and checked the
last line.
The last line of my original restart file (copied from inpcrd file which I
generated using tleap):
* 85.0300000 85.0300000 85.0300000 109.4712190 109.4712190 109.4712190*
The last line of the inpcrd file which I generated after 26ns:
* 85.058 85.058 85.058*
So it is not identical but similar values. What does it mean?
Thanks,
Hirdesh
**********************************************
Hirdesh Kumar
PhD (Molecular Parasitology), MS (Pharmacoinformatics), B. Pharm
AG Frischknecht
*Parasitology - Center for Infectious Diseases*
*University of Heidelberg Medical School*
*Im Neuenheimer Feld 324*
*69120 HeidelbergGermany*
Lab number
:
+49 (0)6221 567438
Mobile number: +49(0) 176 83517413
**********************************************
On Thu, Sep 29, 2016 at 9:05 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Thu, Sep 29, 2016, Hirdesh Kumar wrote:
> >
> > I have a protein-ligand complex in truncated octahedran box. I did minor
> > modifications (deleted two atoms) in the system and want to start a new
> > simulation using the old waterbox information.
> >
> > I tried to use setbox as follows:
> > set var box {85.030 85.030 85.030}
> >
> > however, when i started the new simulation, I found the waterbox changed
> > into "square" .
> >
> > then I changed IFBOX pointer in the prmtop file from 1--> 2.
> >
> > Now the trajectory looks fine.
>
> Check the final line of the rst7 file from the new calculation: is it the
> same
> as the final line from the earlier simulation? If so, you are probably in
> good shape. If not, there are probably problems.
>
> ....good luck....dac
>
>
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Received on Fri Sep 30 2016 - 02:00:02 PDT
