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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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