[gmx-users] Define a new residue in oplsaa

[Shima Arasteh]

Thank you so much.
Shima



________________________________
 From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Saturday, April 14, 2012 9:28 PM
Subject: Re: [gmx-users] Define a new residue in oplsaa
 


Shima Arasteh wrote:
> Dear Justin,
> Thank you so much.
> Are these changes beneficial for other force fields too?
> 

All force fields have to be modified individually and parameters reassigned based on the underlying methodology for parameterization.  Thus, the changes you make in OPLS-AA have no use in other force fields.  The same strategy is used, of course (per the link on adding residues to a force field), but the parameters that are added will be different in each case.

-Justin

> Cheers,
> Shima
> 
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Saturday, April 14, 2012 9:19 PM
> *Subject:* Re: [gmx-users] Define a new residue in oplsaa
> 
> 
> 
> Shima Arasteh wrote:
>  > Dear GROMACS users,
>  > I wanna add add a FOR residue containing atom C and O. In oplsaa force field, the most similar residue to formyl (FOR) is ACE.
>  > How I can change the ACE in .rtp file in oplsaa ff to define FOR residue as a new residue?
>  > I did like this, Is it correct?
>  >
> 
> No.  See below.
> 
>  > [ ACE ]
>  >  [ atoms ]
>  >    CH3    opls_135  -0.180    1
>  >  HH31    opls_140    0.060    1
>  >  HH32    opls_140    0.060    1
>  >  HH33    opls_140    0.060    1
>  >      C    opls_235    0.500    2
>  >      O    opls_236  -0.500    2
>  >  [ bonds ]
>  >    CH3  HH31
>  >    CH3  HH32
>  >    CH3  HH33
>  >    CH3    C
>  >      C    O
>  > [ impropers ]
>  >  CH3    +N    C      O    improper_O_C_X_Y
>  >
>  > [ FOR ]
>  >  [ atoms ]
>  >  HH31    opls_140    0.060    1
>  >  HH32    opls_140    0.060    1
>  >  HH33    opls_140    0.060    1
> 
> A formyl group has only one H atom, since it is an aldehyde.
> 
>  >      C    opls_235    0.500    2
>  >      O    opls_236  -0.500    2
> 
> The charges here for C, H, and O will likely have to be recalculated.  See:
> 
> http://www.gromacs.org/Documentation/How-tos/Parameterization
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
> 
>  >  [ bonds ]
>  >      C    O
> 
> You need a C-H bond as well.
> 
>  > [ impropers ]
>  >  CH3    +N    C      O    improper_O_C_X_Y
>  >
> 
> There is no CH3 in a formyl group.
> 
> -Justin
> 
> -- ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> 

-- ========================================

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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