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

[Justin A. Lemkul]

MARIA ICIAR FRADES ALZUETA wrote:
> 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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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