From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Fri Jul 05 2013 - 12:21:20 CDT
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>> 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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