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

[Justin Lemkul]

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

-- 
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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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