Hi Dan,
I am not quite familiar with using cpptraj. Here is what I did:
>parm 3TNP-with2ADPmg.prmtop
Warning: Could not determine atomic number from mass (3.000000) [DX1 ]
Warning: Could not determine atomic number from name [DX1 ]
(more of these warnings are skipped)
>trajin prod20.rst
[prod20.rst] contains 1 frames.
>autoimage
AUTOIMAGE: To box center based on center of mass, anchor is first
molecule.
>trajout test20.rst
>quit
I could not get any output files. Could you correct me if I did anything
wrong?
Thank you,
Richard
On Wed, Jun 12, 2013 at 5:33 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I suspect that the protein doesn't actually break apart - this is a
> visual artifact caused by 'wrapping' the coordinates. You can use the
> 'autoimage' command in cpptraj to re-image your solute back into the
> primary cell.
>
> -Dan
>
> On Wed, Jun 12, 2013 at 2:56 PM, Hailin Huang <hailin.huang.my.liu.edu>
> wrote:
> > Dear Amber users,
> >
> > I am running a prodution simulation of protein 3TNP in a 10A solvatebox.
> > After about 25 ns of simlutation time, part of the protein drifts out of
> > the solvent box. As the protein falls out further it breaks apart
> > eventually and the fragment comes back in from the other side of the
> > solvent box. Will I solve this problem by simply increasing the size of
> the
> > solvent box? Is there a way to lock the protein within the box? Thanks
> for
> > any help!
> >
> > The input file follows
> >
> > &cntrl
> > imin=0, irest=0, ntx=1,
> > ntpr=2000, ntwx=2000, nstlim=2500000,
> > dt=0.001, ntt=3, tempi=300,
> > temp0=300, gamma_ln=1.0, ig=-1,
> > ntp=0, ntc=2, ntf=2, cut=8,
> > ntb=1, iwrap=1, ioutfm=1,
> > /
> >
> > Regards,
> > Richard
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 19 2013 - 12:00:03 PDT
