Re: fatal error regarding parameters

From: mohammad goodarzi (mo.goodarzi82_at_gmail.com)
Date: Thu Dec 12 2019 - 09:55:08 CST

Thanks Adupa,

I extracted the molecule from a X-ray structure which I dont want to
manipulate much! but thanks a lot for your feedback.
I am trying to take another root on this calculation. I have done it with
Gromacs, the error seems odd with NAMD
Now I am gonna read a bit more to see if I can find out why I get such an
error.

Thanks again
Mo

On Thu, Dec 12, 2019 at 2:40 AM Adupa Vasista <adupavasista_at_gmail.com>
wrote:

> 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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