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 - 13:30:04 PDT
