Re: fatal error regarding parameters

From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Thu Dec 12 2019 - 02:40:47 CST

Dear Mo,

I tried uploading the molecule to CGENFF, it pops up an error: unfulfilled
valence in aromatic subgraph.

Better check your structure and make sure valency satisfies.

Thank you

-vasista

On Wed, Dec 11, 2019 at 11:58 PM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> Hi Mo,
>
> Rather than flaming the tutorials, you really ought to spend some time
> reading the documentation/instructions outside of the tutorials as well.
> You aren't providing the tool the inputs it needs, and its erroring as a
> result. CGenFF asks for a .pdb or a .mol file as an input. What you've
> copied is neither (a .gro file I think?), and so CGenFF can't parse the
> input file.
>
> Slow down, explain what you are trying to do and provide enough detail so
> that others can understand what is going on. From reading between the
> lines, I think you've got a protein/benzene complex, and you'd like to run
> MD in water to do some free energy calculations, right? Step 1 would be to
> get this system running in equlibrium conditions, and then start worrying
> about the other pieces. Can you lay out how you built the system?
> Ideally with a script and a set of input files you could share to make the
> debugging process easier? The readership of this mailing list collectively
> has thousands of years of MD experience, but without a well formulated
> question, we really can't help.
>
> -Josh
>
>
>
> On 2019-12-11 10:26:38-07:00 owner-namd-l_at_ks.uiuc.edu wrote:
>
> Hello,
> I used CGENFF for it. when I import the molecule parameters it gives error
> like error on the first line
> LIGPARGEN GENERATED GRO FILE
> 12
> 1BNZ C00 1 -3.378 0.507 0.291
> 1BNZ C01 2 -3.455 0.482 0.404
> 1BNZ C02 3 -3.297 0.620 0.288
> 1BNZ H03 4 -3.381 0.439 0.207
> 1BNZ C04 5 -3.453 0.568 0.514
> 1BNZ H05 6 -3.518 0.395 0.406
> 1BNZ C06 7 -3.371 0.680 0.512
> 1BNZ H07 8 -3.515 0.548 0.601
> 1BNZ C08 9 -3.296 0.705 0.397
> 1BNZ H09 10 -3.366 0.747 0.596
> 1BNZ H0A 11 -3.234 0.793 0.394
> 1BNZ H0B 12 -3.235 0.641 0.202
> 1.00000 1.00000 1.00000
> then I remove the first line and it give error on BNZ.
> how should the parameter file look like?
> Thanks
> Mo
>
> On Wed, Dec 11, 2019 at 1:51 AM Adupa Vasista <adupavasista_at_gmail.com>
> wrote:
>
>> Use CGENFF to get parameters.
>> Thank You.
>>
>> On Tue, Dec 10, 2019 at 11:45 PM mohammad goodarzi <
>> mo.goodarzi82_at_gmail.com> wrote:
>>
>>> Adupa,
>>> Yes the attached molecule is there too, can you please tell me how to
>>> make the parameter for it?
>>> Thanks a lot
>>>
>>> On Tue, Dec 10, 2019 at 11:28 AM Adupa Vasista <adupavasista_at_gmail.com>
>>> wrote:
>>>
>>>> Are there any other molecules other than protein? If so, then you have
>>>> to add the parameters for that molecule too.
>>>> and while using CHARMM36, better add carb.prm separately instead of
>>>> lipid_prot_carb.prm
>>>>
>>>> On Tue, Dec 10, 2019 at 10:36 PM mohammad goodarzi <
>>>> mo.goodarzi82_at_gmail.com> wrote:
>>>>
>>>>> Hello,
>>>>> I have read a number of posts but none answered me this question.
>>>>> I am getting error as
>>>>>
>>>>> ------------- Processor 0 Exiting: Called CmiAbort ------------
>>>>>
>>>>> Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N287
>>>>>
>>>>>
>>>>> Charm++ fatal error:
>>>>>
>>>>> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N287
>>>>>
>>>>>
>>>>> Abort trap: 6
>>>>> and my parameters are
>>>>> # Force-Field Parameters
>>>>> paraTypeCharmm on
>>>>> parameters ./par_all36_lipid_prot_carb.prm
>>>>> parameters ./par_all36_lipid.prm
>>>>> parameters ./par_all36_prot.prm
>>>>> parameters ./par_all36_na.prm
>>>>> I just don't know what to add more, whatever I add or remove I get the
>>>>> same error
>>>>> Thanks
>>>>> Mo
>>>>>
>>>>
>>>> --
>>>>
>>>> *A.Vasista M.Tech,Department Of Chemical Engineering,*
>>>> *IIT Guwahati.*
>>>>
>>>
>> --
>>
>> *A.Vasista M.Tech,Department Of Chemical Engineering,*
>> *IIT Guwahati.*
>>
>

-- 
*A.VasistaM.Tech,Department Of Chemical Engineering,*
*IIT Guwahati.*

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