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
