Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1

From: Vibhor Agrawal (
Date: Fri Jul 05 2013 - 14:44:31 CDT

Hello Sebastian and Kenno:

Thanks for help:

I changed the parameter file to the par_all27_prot_na.prm
to par_all32_prot_na.prm and its running.I think CMAP correction might have
included in new one.But its running right now


yes I know that there is required parameter is missing !.But thanks anyways
for your help



On Fri, Jul 5, 2013 at 3:16 PM, Rajan Vatassery <> wrote:

> 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 <>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 <
>>> 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
>>>> 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
>>>> < <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--089e0149353875d46d04e0c8ec82--

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