Re: [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  
> 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  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  1LEU CA  10.25 12.011
>>> 
>>> ;residue   7 GLU rtp GLU  q -2.0
>>> 112   opls_283  7GLU CA 37   0.04 12.011
>>> 
>>> 
>>> Choosing 1.   :-(
>>> 
>>> ;residue   1 LEU rtp LEU  q +0.9
>>>   5   opls_299  1LEU CA  1 0.15 12.011
>>> 
>>> ;residue   7 GLU rtp GLU  q -1.9
>>> 112   opls_299  7GLU 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
>> 
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>> 
>> ==
>> --
>> Gromacs Users mailing list
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Re: [gmx-users] selection of start or end terminus

[Justin Lemkul]

On 6/22/16 2:19 PM, Alexander Alexander 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?



OPLS makes special changes to CA in the case of a zwitterion.  Look at the 
contents of the .tdb files and you will see where this comes from.


-Justin


Thanks.
Regards,
Alex

On Wed, Jun 22, 2016 at 8:05 PM, Justin Lemkul  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  1LEU CA  10.25 12.011

 ;residue   7 GLU rtp GLU  q -2.0
 112   opls_283  7GLU CA 37   0.04 12.011


Choosing 1.   :-(

;residue   1 LEU rtp LEU  q +0.9
   5   opls_299  1LEU CA  1 0.15 12.011

;residue   7 GLU rtp GLU  q -1.9
112   opls_299  7GLU 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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [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  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  1LEU CA  10.25 12.011
>>
>>  ;residue   7 GLU rtp GLU  q -2.0
>>  112   opls_283  7GLU CA 37   0.04 12.011
>>
>>
>> Choosing 1.   :-(
>>
>> ;residue   1 LEU rtp LEU  q +0.9
>>5   opls_299  1LEU CA  1 0.15 12.011
>>
>> ;residue   7 GLU rtp GLU  q -1.9
>> 112   opls_299  7GLU 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
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] selection of start or end terminus

[Justin Lemkul]

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  1LEU CA  10.25 12.011

 ;residue   7 GLU rtp GLU  q -2.0
 112   opls_283  7GLU CA 37   0.04 12.011


Choosing 1.   :-(

;residue   1 LEU rtp LEU  q +0.9
   5   opls_299  1LEU CA  1 0.15 12.011

;residue   7 GLU rtp GLU  q -1.9
112   opls_299  7GLU 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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] selection of start or end terminus

[Alexander Alexander]

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  1LEU CA  10.25 12.011

 ;residue   7 GLU rtp GLU  q -2.0
 112   opls_283  7GLU CA 37   0.04 12.011


Choosing 1.   :-(

;residue   1 LEU rtp LEU  q +0.9
   5   opls_299  1LEU CA  1 0.15 12.011

;residue   7 GLU rtp GLU  q -1.9
112   opls_299  7GLU CA 37   0.15 12.011

Many thanks.
Regards,
Alex
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