I did not turn off SHAKE, but I did remove the bond between the H
atoms in this particular water. I didn't know that such a bond really
existed. I always thought that the closed triangle was actually some
visualization bug or something like that. So I guess that is why my
pmemd run failed after all. I'll try doing the tleap routine again
(keeping this particular bond). One thing though. I have noticed that
when I load the protein model to leap, I get a warning saying the the
maximum coordination
for the Hydrogen on this water has been exceeded. Is this to be expected?
Thank you
Fabrício
2012/9/14 Jason Swails <jason.swails.gmail.com>:
> On Fri, Sep 14, 2012 at 3:49 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.
>>
>
> This is expected for many water models (including the TIP series). There
> should be 3 geometric parameters holding the water together (since there
> are 3 atoms). One option is to set bonds between the O and both H atoms
> with an angle connecting them (which seems 'natural' given the bonded
> structure of water). Another option, equally valid, is to define bonds
> between the O and both Hs and to define a bond between the two Hs,
> eliminating the need for an explicit angle term. The 3-bond model is the
> path that is chosen for many water models. (This is also why water
> molecules appear as a closed triangle when viewed through VMD using the
> topology file).
>
> I strongly discourage you from adjusting the water parameters. Note that
> these are rigid water models, meaning they were parametrized with (and
> never intended to be used without) SHAKE (or SETTLE, which is the analytic
> constraint solution for waters). As long as SHAKE is used, what you are
> observing should *never* happen, since the H-H distance will be constrained
> to its original distance. Did you turn off SHAKE?
>
> 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?
>>
>
> It's fine with solvated systems as long as that solvated system is not
> corrupt :). This is a known LEaP bug that arises when separate chains are
> connected via a 'bond' command. The way the prmtop is constructed, all
> atoms connected in a bonded network should appear continuously in the
> topology file. However, LEaP does not re-order atoms after bond commands
> are executed. Which means the ATOMS_PER_MOLECULE and SOLVENT_POINTERS
> sections are incorrect. But the error is subtle and does not seem to
> destroy your simulation...
>
> 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:
>>
>
> Or sander.
>
>
>>
>> ERROR: PMEMD no longer allows constraints in prmtop!
>> | The prmtop must have mbona=nbona, mtheta=ntheta, mphia=nphia.
>>
>> How can I solve this?
>>
>
> Use SHAKE or pick a flexible water model.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Fri Sep 14 2012 - 14:00:06 PDT
