[gmx-users] selection of start or end terminus

[Alexander Alexander]

Thanks for your response.

And then why does "1" go wrong for a single amino acid in  zwitterions
form, as well? Isn't a single amino acid is a kind of peptide with only one
residue?

Thanks.
Regards,
Alex

On Wed, Jun 22, 2016 at 8:05 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/22/16 12:53 PM, Alexander Alexander wrote:
>
>> Dear Gromacs user,
>>
>> In the selection of start or end terminus type for peptide in OPLS_AA
>> force
>> field, what is the diffeece between option 0 and 1 in below list? I am
>> interested in the Zwitterion form, but the option 0 is Zwitterion form if
>> I
>> am not wrong!
>>
>>
>> Select start terminus type for ....
>>  0: NH3+
>>  1: ZWITTERION_NH3+ (only use with zwitterions containing exactly one
>> residue)
>>  2: NH2
>>  3: None
>>
>> And why choosing 1 introduces a tiny amount of charge (0.010 e) in the
>> system and then the whole system in not neutral anymore but 0 is fine. It
>> is clear below the differences and origination of the extra charge in
>> \alpha-C, but how can I fix this if I want to choose 1? Can I simply edit
>> the topol file by replacing the opls_299 to opls_283 ... .?
>>
>>
>> Choosing 0.  :-)
>>
>> ; residue   1 LEU rtp LEU  q +1.0
>>   5  opls_293B      1    LEU     CA      1        0.25     12.011
>>
>>  ;residue   7 GLU rtp GLU  q -2.0
>>  112   opls_283      7    GLU     CA     37       0.04     12.011
>>
>>
>> Choosing 1.   :-(
>>
>> ;residue   1 LEU rtp LEU  q +0.9
>>    5   opls_299      1    LEU     CA      1         0.15     12.011
>>
>> ;residue   7 GLU rtp GLU  q -1.9
>> 112   opls_299      7    GLU     CA     37       0.15     12.011
>>
>>
> pdb2gmx tells you what to do:
>
> "only use with zwitterions containing exactly one residue"
>
> Do you have more than one residue?  If yes, this is a wrong choice.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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