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
--
========================================
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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