From: Vibhor Agrawal (vibhora_at_g.clemson.edu)
Date: Thu Jul 04 2013 - 21:28:54 CDT
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> 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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