[gmx-users] Problem with pdb2gmx for ATP in PDB file

[cpchng at bii-sg.org]

Hi Raj,

   Thanks! Will try this out.
Incidentally, i have John Kerrigan's tutorial with me for quite a while
already.

As for changing names to suit those in the ffgmx.rtp file, i did that but
to no
effect.

Will get back to you on this.

regards,
choon-peng

> 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.
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