[gmx-users][Solved] Removing errors related to missing dihedrals.

[Abhishek Acharya]

Dear Justin.
The errors have now gone away once I followed your suggestion of entering
the missing parameters directly in the topology file. Though there is no
explanation as to why it didn't work with ffbonded.itp, I guess sometimes
ignorance is bliss ;)

Thanks again.
Cheers
Abhishek

>
>
> On 2/14/13 4:15 PM, Abhishek Acharya wrote:
>>
>>
>>> Hello Justin
>>> Thank you very much for your effort and help. I will try adding new
>>> parameter corresponding to the errors. Meanwhile just out of curiosity
>>> and
>>> possible need, what should be done in case no matching parameters are
>>> found for the missing dihedrals? I see that there are 6 fields in the
>>> dihedrals section of ffbonded.itp. How do we calculate these parameters
>>> for new dihedrals ?
>>
>> I wanted to go step by step. I first tried to address the errors 1, 2
>> and
>> 3. So I added the following dihedrals to ffbonded.itp.
>>
>> For Error1:
>> HC     CT     CT     NA      3     -4.09614   5.08775   2.96645
>> -3.95806
>>   0.00000   0.00000
>> from:
>>   HC     CT     CT     NT      3     -4.09614   5.08775   2.96645
>> -3.95806
>>    0.00000   0.00000 ; amine all-atom
>>
>> For Error2
>> OH     CT     CT     NA      3      9.89307  -4.71746   3.67774
>> -8.85335
>>   0.00000   0.00000
>> from:
>> N3     CT_2   CT     OH      3      9.89307  -4.71746   3.67774
>> -8.85335
>>   0.00000   0.00000 ; Chi for Ser & Thr
>>
>> For Error3
>> CT     OS     CT     NA      3     -5.23000   7.32200   6.27600
>> -8.36800
>>   0.00000   0.00000
>> from:
>> CT     OS     CT     N       3     -5.23000   7.32200   6.27600
>> -8.36800
>>   0.00000   0.00000 ; (From wildcard) imidazoles, indoles, purines
>>
>> I expected this to remove the errors 1, 2 and 3. I took care to keep the
>> atomtypes order the same. But this doesn't seem to affect the result. I
>> get the same errors. Any ideas??
>>
>
> None.  If you add new parameters in the right directive, the errors will
> go
> away.  I can offer no explanation as to why that's failing here.  You can,
> of
> course, enter all the missing parameters directly into the topology rather
> than
> having them looked up from ffbonded.itp, but that really shouldn't be
> necessary.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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