[gmx-users] Re: choosing force field

2013-11-10 Thread pratibha 
Thank you Justin for your kind help. The simple reason for considering only
gromos parameter sets is that the parameters for the metal ions (in my
protein) are not defined in other force fields.


On Sat, Nov 9, 2013 at 7:18 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5012376...@n6.nabble.com> wrote:

>
>
> On 11/9/13 12:48 AM, pratibha wrote:
> > Sorry for the previous mistake. Instead of 53a7, the force field which I
> > used was 53a6.
> >
> >
>
> 53A6 is known to under-stabilize helices, so if a helix did not appear in
> a
> simulation using this force field, it is not definitive proof that the
> structure
> does not populate helical structures.  I generally see mixed opinions in
> the
> literature in terms of which Gromos parameter set is the most reliable.
>  As was
> asked by someone else, is there a reason you are only considering Gromos
> parameter sets?  Others may be better suited to your study.
>
> -Justin
>
> > On Fri, Nov 8, 2013 at 12:10 AM, Justin Lemkul [via GROMACS] <
> > [hidden email] >
> wrote:
> >
> >>
> >>
> >> On 11/7/13 12:14 PM, pratibha wrote:
> >>> My protein contains metal ions which are parameterized only in gromos
> >> force
> >>> field. Since I am a newbie to MD simulations, it would be difficult
> for
> >> me
> >>> to parameterize those myself.
> >>> Can you please guide me as per my previous mail  which out of the two
> >>> simulations should I consider  more reliable-43a1 or 53a7?
> >>
> >> AFAIK, there is no such thing as 53A7, and your original message was
> full
> >> of
> >> similar typos, making it nearly impossible to figure out what you were
> >> actually
> >> doing.  Can you indicate the actual force field(s) that you have been
> >> using in
> >> case someone has any ideas?  The difference between 53A6 and 54A7
> should
> >> be
> >> quite pronounced, in my experience, thus any guesses as to what "53A7"
> >> should be
> >> doing are not productive because I don't know what that is.
> >>
> >> -Justin
> >>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 601
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> [hidden email] 
> |
> >> (410) 706-7441
> >>
> >> ==
> >> --
> >> gmx-users mailing list[hidden email]<
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> >>
> >>
>
> >> .
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>
> >>
> >
> >
> > --
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> >
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> [hidden email]  |
> (410) 706-7441
>
> ==
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Re: [gmx-users] Re: choosing force field

2013-11-09 Thread Justin Lemkul 



On 11/9/13 12:48 AM, pratibha wrote:

Sorry for the previous mistake. Instead of 53a7, the force field which I
used was 53a6.




53A6 is known to under-stabilize helices, so if a helix did not appear in a 
simulation using this force field, it is not definitive proof that the structure 
does not populate helical structures.  I generally see mixed opinions in the 
literature in terms of which Gromos parameter set is the most reliable.  As was 
asked by someone else, is there a reason you are only considering Gromos 
parameter sets?  Others may be better suited to your study.


-Justin


On Fri, Nov 8, 2013 at 12:10 AM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5012325...@n6.nabble.com> wrote:




On 11/7/13 12:14 PM, pratibha wrote:

My protein contains metal ions which are parameterized only in gromos

force

field. Since I am a newbie to MD simulations, it would be difficult for

me

to parameterize those myself.
Can you please guide me as per my previous mail  which out of the two
simulations should I consider  more reliable-43a1 or 53a7?


AFAIK, there is no such thing as 53A7, and your original message was full
of
similar typos, making it nearly impossible to figure out what you were
actually
doing.  Can you indicate the actual force field(s) that you have been
using in
case someone has any ideas?  The difference between 53A6 and 54A7 should
be
quite pronounced, in my experience, thus any guesses as to what "53A7"
should be
doing are not productive because I don't know what that is.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

[hidden email]  |
(410) 706-7441

==
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--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Re: choosing force field

2013-11-08 Thread pratibha 
Sorry for the previous mistake. Instead of 53a7, the force field which I
used was 53a6.


On Fri, Nov 8, 2013 at 12:10 AM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5012325...@n6.nabble.com> wrote:

>
>
> On 11/7/13 12:14 PM, pratibha wrote:
> > My protein contains metal ions which are parameterized only in gromos
> force
> > field. Since I am a newbie to MD simulations, it would be difficult for
> me
> > to parameterize those myself.
> > Can you please guide me as per my previous mail  which out of the two
> > simulations should I consider  more reliable-43a1 or 53a7?
>
> AFAIK, there is no such thing as 53A7, and your original message was full
> of
> similar typos, making it nearly impossible to figure out what you were
> actually
> doing.  Can you indicate the actual force field(s) that you have been
> using in
> case someone has any ideas?  The difference between 53A6 and 54A7 should
> be
> quite pronounced, in my experience, thus any guesses as to what "53A7"
> should be
> doing are not productive because I don't know what that is.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> [hidden email]  |
> (410) 706-7441
>
> ==
> --
> gmx-users mailing list[hidden 
> email]
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
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>
>
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> here
> .
> NAML
>


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Re: [gmx-users] Re: choosing force field

2013-11-07 Thread Justin Lemkul 



On 11/7/13 12:14 PM, pratibha wrote:

My protein contains metal ions which are parameterized only in gromos force
field. Since I am a newbie to MD simulations, it would be difficult for me
to parameterize those myself.
Can you please guide me as per my previous mail  which out of the two
simulations should I consider  more reliable-43a1 or 53a7?


AFAIK, there is no such thing as 53A7, and your original message was full of 
similar typos, making it nearly impossible to figure out what you were actually 
doing.  Can you indicate the actual force field(s) that you have been using in 
case someone has any ideas?  The difference between 53A6 and 54A7 should be 
quite pronounced, in my experience, thus any guesses as to what "53A7" should be 
doing are not productive because I don't know what that is.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Re: choosing force field

2013-11-07 Thread pratibha 
My protein contains metal ions which are parameterized only in gromos force
field. Since I am a newbie to MD simulations, it would be difficult for me
to parameterize those myself.
Can you please guide me as per my previous mail  which out of the two
simulations should I consider  more reliable-43a1 or 53a7?  
Thanks in advance.

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