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

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Fri Jul 05 2013 - 15:47:58 CDT

The official parameter releases contain all the necessary terms and they
always have. You must have been using an adulterated version of
par_all27_prot_na.prm . Also, your simulation did not "run for a while",
it crashed before NAMD got to the actual MD code. It's hard to help you if
you provide misleading information.

By the way, it would be more optimal to use the CHARMM36 topology files
for psf generation and the CHARMM36 parameter files for NAMD simulation,
because there are important improvements in the force field. The new
versions can be freely downloaded from
http://mackerell.umaryland.edu/CHARMM_ff_params.html

On 07/05/2013 03:44 PM, Vibhor Agrawal wrote:
> 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
>
> @Rajan:
>
> yes I know that there is required parameter is missing !.But thanks anyways
> for your help
>
>
> Thanks
>
> vibhor
>
>
> On Fri, Jul 5, 2013 at 3:16 PM, Rajan Vatassery <rajan_at_umn.edu> 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 <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

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