[gmx-users] oligoglycines

[nishap.patel at utoronto.ca]

Thanks Justin!

Nisha P


Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
>
> nishap.patel at utoronto.ca wrote:
>> Hello,
>>
>>   I want to simulate n-glycines (diglycine, triglycine..etc) I   
>> tried to get the structure from PRODRG, but the program adds H's on  
>>  the N-terminal instead of on C- terminal. Is there another program  
>>  I could use, or a site where I could get the structure of   
>> oligoglycines? For example, diglycine (NH2-CH2-CO-NH-CH2-COOH), but  
>>  PRODRG gives me ((NH3-CH2-CO-NH-CH2-COO)
>>
>
> Protonation state is easy to change with pdb2gmx when writing your
> topology. Use -ignh and/or -ter to set the proper state.  You can also
> tune this with PRODRG (see the FAQs regarding ADDHYD and DELHYD
> commands), but since you can do it all with Gromacs anyway, it
> shouldn't be necessary.
>
> -Justin
>
>> Thanks!
>>
>> Nisha P
>>
>
> -- 
> ========================================
>
> 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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