From: Sebastián Gutiérrez (segumal_at_gmail.com)
Date: Fri Jul 05 2013 - 14:03:08 CDT
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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