[gmx-users] how to parametrize Phos. Thr TPO

[Justin A. Lemkul]

nahren manuel wrote:

<snip>

> ----
> but i get the following error
>  * * * * * 
> Generated 380 of the 1326 non-bonded parameter combinations
> ERROR 0 [file "top_A.itp", line 16530]:
>   No default Proper Dih. types
> ERROR 0
>  [file "top_A.itp", line 16531]:
>   No default Proper Dih. types

Then you haven't added all of the proper dihedrals for that particular molecule 
(phosphates are tricky).  There is a parameter set (ffG43a1p) that has a 
properly-derived set of parameters for phosphorylated amino acids in the User 
Contributions on the web site.

I recall that not all of the formatting was quite right in these files (they 
were designed for use with Gromacs 3.1.x, IIRC), so if you encounter errors you 
can contact me off-list and I can send you re-formatted files that I have gotten 
to work.

-Justin

> Excluding 3 bonded neighbours for Protein_A 1
> Excluding 3 bonded neighbours for Protein_B 1
> NOTE:
>   System has non-zero total charge: -1.999996e+00
> 
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
> #   G96BONDS:   5789
> #  G96ANGLES:   8462
> #      PDIHS:   3040
> #      IDIHS:   2893
> #       LJ14:   9248
> 
> -------------------------------------------------------
> Program grompp, VERSION 3.3.2
> Source code file: grompp.c, line: 1182
> 
> Fatal error:
> There were 2 errors in input file(s)
> -------------------------------------------------------
> 
> "Ich Bin Ein Berliner" (J.F. Kennedy)
> * * * * * * 
> 
> Kindly advice
> nahren
> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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