Hi Fabricio,
I think Leap assumes you will have triangulated rigid waters unless you
tell it otherwise. I.e. a bond between HW and HW and shaken such that you
do not need the angle parameter.
Try setting
set default FlexibleWater on
in leap and then try building your prmtop again and see if you get the
angle term written.
All the best
Ross
On 9/14/12 12:49 PM, "Fabrício Bracht" <bracht.iq.ufrj.br> wrote:
>Hello. I have been trying to figure out why my simulations of a zinc
>protein with a water molecule bound to the zinc atom were failing
>without any warning. I think I found out what the problem is. While
>inspecting the the catalytic site (the residues from the active site
>were parameterized using the MTK++ procedure. To see more details on
>this, see http://archive.ambermd.org/201208/0174.html ), I discovered
>that the angle between the H1-O-H2 atoms of the water molecule was
>practically zero. I mean, they really collapsed onto each other. I
>think the only thing that was holding them from actually collapsing
>was the small vanderwalls parameters I introduced in order to solve
>another problem regarding the charge distribution...etc (not really
>the discussion here). The problem is that the parameters for this
>particular angle is described in the .frcmod file. The line :
>
>HW-OW-HW 103.000 104.520
>
>should have worked, right?
>When I check the parameters of the prmtop file using parmed.py, I find
>that there are no angle parameters for these 3 atoms. None whatsoever.
>I tried introducing them with parmed.py by using the command
>setAngles, but when I try to save the modified prmtop file I get:
>
> Outputting Amber topology file 1g5c_pre1.prmtop
>MoleculeError: Molecule atoms are not contiguous!
>
>Does parmed.py have problems with solvated systems?
>
>Then I tried introducing restraints while doing the tleap routine, but
>since I am using pmemd.cuda, pmemd kindly told me that restraints are
>no longer supported by pmemd:
>
> ERROR: PMEMD no longer allows constraints in prmtop!
>| The prmtop must have mbona=nbona, mtheta=ntheta, mphia=nphia.
>
>How can I solve this?
>Thank you
>Fabrício
>
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Received on Fri Sep 14 2012 - 13:00:02 PDT
