Jose Borreguero wrote:
Dear Gromacs users,
Im new to gromacs and I'm following a tutorial
(http://nmr.chem.uu.nl/~tsjerk/course/molmod/). Unfortunately, the
tutorials doesn't say anything about how to update the topology file
after using 'genion' to replace a few water molecules with ions.
I manually edited the topology file and updated the number of water
molecules and added the number of ions:
Using the -p flag will make all the necessary changes automatically.
[ molecules ]
; Compound #mols
Protein_chain_A 1
SOL 7791
Na+ 26
Cl- 23
But then when I tried to preprocess the structure with grompp, I got an
error:
Fatal error:
No such moleculetype Na+
Assuming you're using a new version of Gromacs (4.5.x), the naming scheme has
changed. Check the ions.itp for the force field you've chosen to use to set
proper names.
-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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