Hi Fabrício,
I suspect you're better off not having it called WAT. Otherwise, pmemd will expect it to behave like a rigid 3-point water.
Also, I trust you're not overriding the name WAT with the WATNAM variable.
Cheers,
Ben
On 15/09/2012, at 8:16 AM, Fabrício Bracht wrote:
> The tleap procedure worked. But now I get from pmemd :
>
> Error: Fast 3-point water residue, name and bond data incorrect!
>
> Ps: I've renamed the residue WAT.
>
> Thank you
> Fabrício
>
> 2012/9/14 Fabrício Bracht <bracht.iq.ufrj.br>:
>> It worked. Thank you
>> Best regards
>> Fabrício
>>
>> 2012/9/14 Fabrício Bracht <bracht.iq.ufrj.br>:
>>> Do I have to rename this particular water residue to WAT or something
>>> like that. Currently it is called OH1. The prep file states that it is
>>> a TIP3P water like molecule, bu it is not named as such. Is this a
>>> problem?
>>> Thank you
>>> Fabrício
>>>
>>> 2012/9/14 Ross Walker <ross.rosswalker.co.uk>:
>>>> 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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>>>>
>>>>
>>>>
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Received on Fri Sep 14 2012 - 14:00:05 PDT
