[gmx-users] AMBER and gromacs atoms renaming

Justin A. Lemkul jalemkul at vt.edu
Sun Aug 10 18:56:47 CEST 2008

Ragnarok sdf wrote:
> 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.

You could create (in a sense) an "alias" for the problematic residues.  That is, 
the AMBER equivalent of LYS is LYN, and for LYSH is LYP.  What I've done with my 
.rtp files is to copy the section that designates LYN and make a duplicate entry 
that is headed [ LYS ].  Similarly, you can apply this type of manipulation to 
ASP, GLU, CYS, HIS, and anything else you find that has different nomenclature. 
  You would then have to make corresponding changes in the .hdb file, as well. 
Using pdb2gmx -ignh in conjunction with the .hdb file will eliminate the need to 
manually re-name all hydrogen atoms.  If you do this, the only names you will 
have to change are the N- and C-termini.

If you don't want to do all that, find and replace within vi is quite simple, 
for example:


will find and replace all LYS with LYP.  If you need varying protonation states, 
this can be more tedious.  Otherwise, altering all the residue names should only 
take a few minutes per file.

Another option is to use xleap to prepare your input.  It is now freely 
available as part of the AmberTools package.  Using xleap should give all your 
atoms the proper AMBER nomenclature.


> 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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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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