[gmx-users] for a single amino acid with NH3+ and COO- terminii, pdb2gmx gives a total charge of -1.1 in OPLSAA ?

[maria goranovic]

that makes sense, thank you Justin

On Tue, Jun 1, 2010 at 4:01 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> maria goranovic wrote:
>
>> I tried pdb2gmx with an alanine pdb file, with options 5 (opls force
>> field),  0 (NH3+ n-terminus) and 0 (COO- C-terminus). When I run grompp on
>> the output from pdb2gmx, I get a total charge of -1.1. Any ideas why this
>> happens?
>>
>> The same problem is not there if one looks at a dipeptide. Why the problem
>> for a single amino acid? It looks like when pdb2gmx applies patches for the
>> N-terminus and C-terminus to the ends of a protein, it changes atom types
>> for the peptide backbone. If one uses a single amino acid, the patches are
>> applied to the same residue, and hence the odd -1.1 charge? If this is so,
>> is this not a bug?
>>
>>
> This is not a bug.  You're choosing the wrong termini.  With OPLS, there is
> a "zwitterion" terminus option that you should be using, since a single
> amino acid with two charged termini is a zwitterion.
>
> -Justin
>
>
>  Thank you for inputs,
>>
>> -maria
>>
>>
>> --
>> Maria G.
>> Technical University of Denmark
>> Copenhagen
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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-- 
Maria G.
Technical University of Denmark
Copenhagen
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