Jose Borreguero wrote:
Hi Justin, thanks for your reply!
I appended '-p protein.top' to genion. File protein.top was
automatically updated by insertion of the following lines at the end of
the file:
/[ molecules ]
; Compound #mols
Protein_chain_A 1
SOL 7791
NA+ 26
CL- 23/
My solvated PDB, protein-solvent.pdb contains lines like these:
ATOM 24543 NA NA+ 8043 50.712 66.452 12.341 1.00 0.00
Now when I run grommp, I get the error
/Fatal error:
No such moleculetype NA+/
I checked file gromos45a3.ff/ions.itp. The sodium is included in this
fashion:
/[ moleculetype ]
; molname nrexcl
NA 1
[ atoms ]
; id at type res nr residu name at name cg nr charge mass
1 NA+ 1 NA NA 1 22.9898/
It seems the naming convention of ions.itp is different than that of
protein.top and protein-solvent.pdb. I changed protein.top and
What was your exact genion command? If you tell genion to use "-pname NA+"
(which is wrong) you get this result. Note that the error says the moleculetype
"NA+" is not found; the moleculetype name is "NA" instead.
protein-solvent.pdb to match the naming of ions.itp. Then when I run
grompp I get the error:
/ERROR 1 [file protein.top, line 7228]:
ERROR: One of the box lengths is smaller than twice the cut-off length.
Increase the box size or decrease rlist./
The puzzling thing is that line 7228 of protein.top is the last line of
the file, that is,
CL 23
So the error message is not much help :(
The problem comes from the coordinate file and settings of the .mdp file; they
are somehow incompatible such that they would cause a violation of the minimum
image convention. Why the error points to the .top I cannot say.
-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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