From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Aug 09 2007 - 20:09:29 CDT
Hi Philip,
sorry, I had it muddled in my own head; the usage in the topology files
is correct, and as long as you're using it the same way, things should
work fine. Please note that in psfgen DOUBLE is treated exactly like
BOND, since any differences are taken care of by the parameters. It
would be good to check your psf, though, and see if any of the dihedrals
are double counted. I believe this could happen, for example, if you
both explicitly specify a dihedral and indicate autogeneration (although
I'd have to test that to be sure -- I know I've seen this error show up
before when I did something along those lines).
Best,
Peter
Philip Peartree wrote:
> Hi Peter,
>
> I'm not sure what you mean in your last sentence, as far as I can see,
> in all
> residues in the topology file double is used in place of the bond
> keyword to
> specify a double bond instead of a single bond. Is this not correct
> usage?
>
> Unfortunately I don't have the psf at hand, but I will check it tomorrow.
>
> Philip
>
>
> Quoting Peter Freddolino <petefred_at_ks.uiuc.edu>:
>
>> Hi Philip,
>> I honestly don't know if charmm does any sort of internal checking to
>> avoid this being a problem. I can suggest looking in your psf file at
>> any dihedral terms involving four CA atoms, and see if any of them are
>> listed repeatedly. If so, you may want to make sure that in your
>> topology file no bonds are doubled up, and that you're not applying a
>> patch that lists an already existing bond. Also, you should make sure
>> that the double keyword is not being used in the topology file without
>> also specifying a bond for the same two atoms; iirc correctly psfgen
>> doesn't like this.
>> Best,
>> Peter
>>
>> Philip Peartree wrote:
>>> Hi Peter,
>>>
>>> I generated the psf using the VMD psf gen tool (the graphical one, not
>>> the
>>> commandline version) and the topology file is one of my own making
>>> (essentially
>>> Charmm27 but with a few additional residues (I'm simulating a
>>> quinoprotein,
>>> which contains a modified tryptophan) I'm assuming that the problem is
>>> with
>>> that residue, but the thing puzzling me is that it worked fine in c31
>>> itself.
>>>
>>> Philip Peartree
>>>
>>>
>>>
>>> Quoting Peter Freddolino <petefred_at_ks.uiuc.edu>:
>>>
>>>> Hi Philip,
>>>> just to verify, could you please let us know how you generated your
>>>> psf?
>>>> And which topology file are you using?
>>>> Best,
>>>> Peter
>>>>
>>>> Philip Peartree wrote:
>>>>> Dear All
>>>>>
>>>>> Upon running (an albeit) basic simulation (Minimisation, I
>>>>> received the
>>>>> following error:
>>>>>
>>>>> FATAL ERROR: Multiplicity of Paramters for diehedral bond CA CA CA
>>>>> CA of 1
>>>>> exceeded
>>>>>
>>>>> I am aware that several messages of this type have been posted to
>>>>> this list, but
>>>>> none have fully detailed a positive outcome. From what I have read
>>>>> of other
>>>>> messages, this is something to do with a wrongly typed bond
>>>>> somewhere in the
>>>>> topology file (I am using a Charmm type topology). However, this
>>>>> topology/parameter set worked fine in Charmm31 (I have decided to
>>>>> start running
>>>>> in NAMD since it was taking about 3.5 months to run a 10 ns
>>>>> simulation!!)
>>>>>
>>>>> What should I do about correcting this, since the bonds are
>>>>> correctly defined in
>>>>> the topology (as far as I know)
>>>>>
>>>>> Philip Peartree
>>>>> Sutcliffe Group
>>>>> University of Manchester
>>>>>
>>>>
>>>
>>>
>>
>
>
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