From: Philip Peartree (P.Peartree_at_postgrad.manchester.ac.uk)
Date: Thu Aug 09 2007 - 18:50:06 CDT
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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