[gmx-users] AMBER and gromacs atoms renaming

Ragnarok sdf fabracht1 at gmail.com
Sun Aug 10 18:05:17 CEST 2008

Hi, I am running a simulation of a protein DNA complex, and for this i
am using AMBER99 forcefield. The problem is that every complex I need
to run, I have to rename several residues and atoms, especially
hydrogen atoms one by one (well, actually using replace tool). And
this takes hours to get done.
Is there any shortcut I can use, like a software that prepares my pdb
files for an AMBER run, or something close to that?
If not, Ill just keep doing things by hand.
Thank you
Fabrício Bracht

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