[gmx-users] proper and improper dihedrals in topology file from other ff

[Justin Lemkul]

On 3/21/13 10:20 PM, 라지브간디 wrote:
> Dear gmx users,
>
>
> I am MD simulation for heme ligated protein where i given all bond and angle, dihedral information in topology file created by pd2gmx ( gromos43a1).
>
>
> However, i do not know how to interpret the proper and improper dihedrals in topology file? I have looked over the .rtp file and found that gromos mentioned like
>
> example:
>
>
> [ impropers ]
> ;  ai    aj    ak    al   gromos type
>     C2    N1    N3   NA2     gi_1
>    NA2  HA21  HA22    C2     gi_1
>     N3    C2    C4   HA3     gi_1
>
>
> But the the parameter  I use from literature where its in charmm and amber format as they mentioned the torsions like following way.
>
>
> Improper
> CPB-X-X-CR1E    90.0   0.0
> CC - X-X-NB       18.3     0.0
>
>
> ...............etc
>
>
> How do i use this improper to utilize in gromos?
>

Every force field has small differences in format.  Look at ffbonded.itp for 
43A1 and you will see #define statements that correspond to bonds (gb_*), angles 
(ga_*), etc.  Those macros just mean "substitute this information here."  It's 
shorthand.  So either you can introduce a new definition in ffbonded.itp or just 
type the parameters in manually according to the format specified in the manual.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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