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 - 13:30:03 PDT
