Hi,
Sorry for sending this again. My earlier mail got marked up.
I used this command to remove water in the pdb file that I obtained from the initial prmtop and inpcrd files.
grep -v 'WAT' 2a6_init.pdb > 2a6_init_nowat.pdb
I was then able to load 2a6_init_nowat.pdb and then the trajectory file that I obtained through ptraj imaging with nobox, nowater in vmd. It worked very well.
I thank you all for taking time to get me through this problem.
Jaya.
On 05/12/10, Jason Swails <jason.swails.gmail.com> wrote:
>
> 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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> > >
> >
> >
> >
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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 Thu May 13 2010 - 09:00:05 PDT
