Hi,
On Thu, Jan 15, 2015 at 11:31 AM, Atila Petrosian
<atila.petrosian.gmail.com> wrote:
> 1) Water molecules are shown as a triangle (there is a bond between
> Hydrogen atoms). I don't know the reason of this issue.
This is normal. Water models like TIP3P are rigid; instead of an angle
term for H-O-H there is a bond between the two hydrogen atoms (you can
check this yourself with parmed.py or cpptraj).
> 2) Most of water molecules have went out of box. To solve this issue,
> I re-imaged molecules back into the box as follows:
Try the 'autoimage' command in cpptraj instead of 'center' and 'image'
and see if that fixes your imaging problems.
-Dan
>
> trajin prod.mdcrd
> trajout prod-reimage.mdcrd
> center :1-98
> image familiar
>
> When I see prod-reimage.mdcrd file using vmd, water molecules back into the
> box.
> There are 2000 frames in mdcrd file. In more precise view, I found that in
> two frames (1084 and 1085), protein molecule have went out of box. please
> note the figure in the following link
> (https://www.dropbox.com/s/kmndaeeee07znk0/d.png?dl=0).
>
> I re-imaged molecules, so what is the reason of that protein molecule goes
> out of box in two frames during the trajectory?
>
> I calculated rmsd. rmsd values are very high in these two frames.
>
> How to resolve this problem?
>
> Best wishes,
> Atila
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jan 15 2015 - 11:00:03 PST
