On Thu, Mar 07, 2019, Hadi Rahmaninejad wrote:
>
>I have a silica system which I solvated it in water by "psfgen" and then
>converted it to amber using "chamber" in "parmed". In coordinate file I
>dont have that line at the end which shows the dimension and angles of the
>box,
Odd, and suggests that something went wrong with the conversion step.
Is the psf file in a periodic box?
> so that I added that line by myself:
>50.0000000 50.0000000 50.0000000 90.000000 90.0000000 90.0000000
>the "50" that I defined is the length of my system in any direction.
How sure are you that 50 is correct? Have you visualized the system,
including the surrounding periodic box boundary? Do you see bad
overlaps?
>minimized that using:
>The bonds start to expand (even water bonds) and then the system exploded
>after about 115 frames, and I got this error:
Use the "check" command in cpptraj to look for bad overlaps in the
starting structure. What is the profile of energy vs. minimization
step? Are there any "****" fields in your mdout file?
It's really hard to even guess about all the things that could have gone
wrong here, since you are doing a very non-standard calculation (silica,
starting with CHARMM (I guess?), adding box dimensions by hand, etc.)
It's not clear what sort of "silica" you have, but note this (which may
or may not be relevant): Amber does not allow covalent bonds between
atoms in different periodic boxes, and is unlike CHARMM in this regard.
...hope this helps....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 08 2019 - 06:30:03 PST
