[gmx-users] RE: Converting from AMBER to GROMACS
feenstra at few.vu.nl
Tue May 3 19:36:34 CEST 2005
Jordi Camps wrote:
> Hi all!
> Paste back the coordinates of my original file is my next step, but because
> of the change in atom name AND number I must compare the original
> coordinates and the new coordinates and select the closest one for
> substitution. Which method do you think that will be more precise? Minimal
> difference? Minimal root mean squared?
> This cold be avoided if someone can ensure that pdb2gmx ALWAYS change O->O2
> and OXT->O1. Then I could select the atoms by name, which is easier and we
> won't be guessing.
Perhaps if you add entries to 'xlateat.dat' which sits in your GMXDATA
directory somewhere. Otherwise, you could hack away the code that
removes this duplicate oxygen.
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