[gmx-users] selection of start or end terminus

[Erik Marklund]

Dear Alex,

A single amino acid is not a peptide sine it has no peptide bonds.

Kind regards,
Erik

> On 22 Jun 2016, at 20:19, Alexander Alexander <alexanderwien2k at gmail.com> wrote:
> 
> 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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