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

[Raj Badhan]

Hi
I did try to adjust the names when I was having problems, but I 
found by just getting the GRO files from prodrg and incorporting the 
two with all the columns aligned as I mentioned before this worked 
and gromacs recognized atp.


> Chng Choon Peng wrote:
> 
> >Dear all users,
> >
> >  I've been searching the mailing list to find the work around for getting
> >pdb2gmx to recognize ATP. Keep getting this error:
> >
> >Fatal error: Atom PG in residue ATP 252 not found in rtp database
> >             while sorting atoms
> >
> >Do I need to rename them, like use APG instead of PG?
> >Tried that but doesn't seem to work either.
> >
> >Been trying for quite a while, but to no result.
> >Can anyone help? Thanks!
> >
> >
> >Regards,
> >Choon-Peng
> >
> >  
> >
> The name of atoms in .pdb need to be the same of the .rtp file.
> 
> []'s
> 
> -- 
> Alexandre Suman de Araujo
> asaraujo at if.sc.usp.br
> UIN: 6194055
> IFSC - USP - Sa~o Carlos - Brasil
> 
> 
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Raj Badhan
Postgraduate researcher
School of Pharmacy and Pharmacetical Science
The University of Manchester
Manchester, UK.