Hello. Now it seems to work. I ran I minimization and a short md
simulation just to check if there are no technical problems. Here is
what I did. I've changed back the name of the water residue to OH1 and
left the bond between the H atoms unchanged. Did not turn flexible
water on, since I did not do this for the other system with a hydroxyl
instead of a water molecule, but if you think this is necessary,
please let me know. Generated the prmtop file again and all seems to
be in good shape.
Thank you again
Cheers
Fabrício
2012/9/14 Fabrício Bracht <bracht.iq.ufrj.br>:
> 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 - 14:30:05 PDT
