[gmx-users] How to make ADP parameters

Zhiguo Liu zgliu at iris3.simm.ac.cn
Thu Mar 11 11:31:00 CET 2004

Dear gmx-users ,

    The following is what I searched from the list archive:

> Hi
> I had the same problem....this is how you fix it:
> Put your atps into prodrg, which will assign charges and create a
> gro file for the atp.
> The copy and paste this into your protein gro file at the bottom.
> BUT, you have to make sure that all the colums are alligned as so:
>   462ALA      O1  4469   1.152   3.417   4.013
>   462ALA      O2  4470   1.037   3.296   4.189
>   463ADP    O2B 4471   4.461   3.235   4.392
>   463ADP      PB 4472   4.312   3.238   4.332
>   463ADP    O3B 4473   4.215   3.194   4.434
>   463ADP    O1B 4474   4.273   3.370   4.280
>   463ADP    O3A 4475   4.322   3.141   4.216
>   463ADP      PA 4476   4.430   3.112   4.10
> Essentially, you simply have to make sure that all the colums align
> downwards and accross, and follow how they align in your protein.
> If you dont do this, you will get strange errors when trying to
> solvate your box.
> Follow the drug-enzyme tutorial and that will explain in detail how
> to use prodrg and combine gro and itp files into your protein. YOU
> WILL NEED to read this before you can incorporate your files.
> Hope that helps
> Raj Badhan
> Postgraduate researcher
> School of Pharmacy and Pharmacetical Science
> The University of Manchester
> Manchester, UK.

It seems not clear about how to align other atom of ADP, e.g., the C atoms and other O atoms. 

I modified my coordinates file as above, but when I do "grompp" , I encountered such error messages:

"Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 182 of the 1128 non-bonded parameter combinations
Cleaning up temporary file grompp804482
Fatal error: Atomtype 'OS' not found! "

I checked my complex's gro file, but find no such 'OS' type atom.

(In my case, a modified forcefield named "ffG43a1p" was used, which added parameters for phosphorylated residues. )

Any advice is welcome!

Best Regard!
                                 Zhiguo Liu
                                 Chinese Academy of Science
                                 zgliu at iris3.simm.ac.cn

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