[gmx-users] Adding a residue

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 13 19:51:36 CEST 2009

Smith, Chanel Chonda wrote:
> Hello,
>     I am currently using GROMACS 4.  When trying to process the pdb file
> with pdb2gmx, an error message came up stating that a particular residue was
> not recognized by the residue topology database.  I then tried to adding a
> molecule in the ff....rtp file and adding the name in aminoacids.dat.  This
> did not work either.  The residue that I need to add is a nonprotein.  Could
> you tell me how I can add this residue to the database and therefore allowing
> me to process the pdb file?

You've followed the correct procedure.  If the new residue is a ligand of some 
sort, it may just be easier to create an .itp file for it (using one of the 
user-contributed programs, or something like PRODRG).

If you still want to use the .rtp approach, provide more details, like the 
actual .rtp entry and the exact error message that you're getting from pdb2gmx.


> Thanks,
> Chanel King
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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