From: Rajan Vatassery (rajan_at_umn.edu)
Date: Fri Jul 05 2013 - 14:16:59 CDT
Vibhor,
You indeed are missing the required parameters from the file you are using.
Any time you get the "UNABLE TO FIND XXXXXX FOR YYYYYY" you are missing
parameters.
Check the literature for these parameters, and there are a lot of threads
on this listserve that will be helpful as well.
Rajan
On Fri, Jul 5, 2013 at 2:03 PM, Sebastián Gutiérrez <segumal_at_gmail.com>wrote:
> Vibhor,
>
> could you attach the output log file that NAMD writes?
> That could help to solve your issue.
>
>
>
> On Fri, Jul 5, 2013 at 1:21 PM, Kenno Vanommeslaeghe <
> kvanomme_at_rx.umaryland.edu> wrote:
>
>> I don't understand how it can run OK "for a while" and then suddenly lose
>> an existing parameter. I don't know much about NAMD's inner workings, but
>> it sounds to me that either your NAMD input is doing something very
>> nontrivial, or you just *might* have hit a bug. Are you running a "nightly
>> build"?
>>
>> On 07/04/2013 10:28 PM, Vibhor Agrawal wrote:
>>
>>> Hello Kenno:
>>>
>>> I'll be more detailed
>>>
>>> I homology modelled my protein and capped the the ends with ACP and
>>> CT3.Then created the psf After inserting in into POPC bilayer and
>>> ionizing
>>> it .I prepared my system for NAMD simulation.First step was to melt the
>>> lipid tail.I used the par_all27_prot_lipid.prm parameter file.The
>>> simulation ran for a while after it gave me error as
>>>
>>> UNABLE TO FIND CROSSTERM PARAMETERS FOR C NH1 CT1 C NH1 CT1 C NH1 for
>>> ATOMS (ATOMS 32838 32839 32840 32849 32842 32843 32844 32851)
>>>
>>> I checked the ATOMS in pdb file they are of residues are Proline and SER
>>> in the pdb fille.Is something missing in the parameter file or removing
>>> the crossterm would be better way??
>>>
>>> Thanks
>>>
>>>
>>> Vibhor
>>>
>>>
>>> On Thu, Jul 4, 2013 at 8:49 PM, Kenno Vanommeslaeghe
>>> <kvanomme_at_rx.umaryland.edu <mailto:kvanomme_at_rx.umaryland.**edu<kvanomme_at_rx.umaryland.edu>>>
>>> wrote:
>>>
>>> If this happens after some simulation steps (as opposed to right at
>>> the start), then I doubt removing the cross term is the correct
>>> answer. The error message you're getting is more likely a symptom of
>>> another issue. That's all I can say with the available information.
>>>
>>>
>>>
>>> On 07/04/2013 03:31 AM, Vibhor Agrawal wrote:
>>>
>>> Hello All:
>>>
>>> I started to run the NAMD simulation with my membrane protein
>>> and I
>>> witnessed the error during the melting of the lipid tail .There
>>> came a
>>> fatal error with the cross term of C NH1 CT1 C NH1 CT1 C
>>> NH1 in
>>> specific atom.Is it due to the parameter file ? I'm using
>>> the par_all27_prot_lipid.prm.?
>>> should I delete the cross term from my psf file or use a
>>> different
>>> parameter file??
>>>
>>> Please help.Any kind of guidance will be really helpful
>>>
>>> Thanks
>>>
>>> Vibhor Agrawal
>>> Graduate student
>>> Clemson University
>>>
>>>
>>>
>>>
>>
>
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