[gmx-users] pdb2gmx of nucleic acids with ffamber03 force field

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 31 16:57:35 CEST 2011

> Dear all,
> I am trying to pdb2gmx a a pdb file gcaa.pdb having nucleic acids using 
> amber force field 03:
> pdb2gmx -ff amber03 -f gcaa.pdb -o rna.pdb -p rna.top -water tip3p
> I have two questions:
> 1.
> The ffamber03.rtp file specifies that O2 from should be O to be 
> recognized by the rtp file. When one substitutes this atom the program 
> complains:
> Fatal error:
> Atom O in residue RC 4 was not found in rtp entry RC with 31 atoms
> while sorting atoms.
> Keeping the original pdb O2 works fine, althought O2 is not in the 
> ffamber03.rtp  file. Is this fine?

The atom name (O2) and type (O) are distinct.  Names have to match so that 
pdb2gmx can assign the correct type.

> 2.
> When doing: editconf -f gcaa.pdb -o this.pdb
> The residues named H2'1 as mapped in the .rtp file they became 1H2'. The 
> pdb2gmx works fine but I do not know how it works if the new 1H2' is not 
> in the ffamber03.rtp file.

Hydrogen nomenclature can be annoying.  Everyone seems to have their own 
standard.  If the topology was produced without issue, then the parameters 
applied to the structure are fine.



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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