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

[Anton Feenstra]

cpchng at bii-sg.org wrote:
> 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.

You should be aware that pdb2gmx has several rules for changing atomnames
(and residue names as well). This is necessary to be able to read many of
the naming variations found in .pdb files. The atom re-naming rules are
in $GMXDATA/top/xlateat.dat (the residue renaming rules are hardcoded, I
am afraid...).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
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|  _   _  ___,| K. Anton Feenstra                                     |
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