Hello,
Don't forget that you are stripping the water. If you haven't already, you
have to remake the topology file without the water residues present, or you
will get the effect you're seeing (I'm assuming this is what's happening).
You can load your prmtop file into rdparm, use the command stripwater, and
save the new prmtop to use with VMD, but it's too old to be used for
calculations in my experience. (And you can't use Amber 7 parm, you have to
use the other parm in VMD)
Another alternative is to use one of the PDB files you created and run it
through leap to get the prmtop (this would probably be easier if you don't
have any custom ligand and/or custom residues).
Hope this helps,
Jason
On Wed, May 12, 2010 at 4:23 PM, Jayalakshmi Sridhar <jsridhar.xula.edu>wrote:
> My earlier mail got marked up. So, I am resending it.
> I ran the script for 5 frames with trajout to pdb files as suggested. I got
> 5 pdb files. Each of them loaded normally in vmd without any streaks. The
> avg structure in the earlier run and in the present 5 frame run looked
> normal in vmd.
> Jaya.
>
> On 05/12/10, Thomas Cheatham III <tec3.utah.edu> wrote:
> >
> >
> > > After putting the trajout statement after the strip command, I do not
> > > see the box shape. The number of frames are also consistent with 2400
> > > frames. But the atoms are still streaking in the vmd display. I am
> > > attaching a picture of the image as jpg file. Jaya.
> >
> > The position of the trajout, in all versions of ptraj, is irrelevant.
> > What is likely true is that there is a mismatch between your trajectory
> > and your loaded prmtop (as mentioned by Prof. Simmerling). (By the
> > way, from the scripts shown previously you loaded AMBER trajectory format
> > files, not binpos).
> >
> > The offsets seen in your movie are consistent with the AMBER trajectory
> > not having box information, but the prmtop having box information (or
> > vise-versa). In this case, usually the first frame (in a VMD movie)
> looks
> > OK, and subsequent ones get shifted.
> >
> > To verify things are OK and its a prmtop mismatch, do your script the
> same
> > for ~5 frames...
> >
> > trajin mdcrd 1 5 1
> >
> > and change the trajout to PDB files and look at these.
> >
> > trajout tmp-pdb pdb
> >
> > (or also look at your avg.pdb)
> >
> > --tec3
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber (
> http://lists.ambermd.org/mailman/listinfo/amber)
> >
>
>
>
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>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed May 12 2010 - 14:30:04 PDT
