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 <[email protected]>
*To:* Shima Arasteh <[email protected]>; Discussion list for
GROMACS users <[email protected]>
*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
========================================
--
gmx-users mailing list [email protected]
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
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
