[gmx-users] No molecule type K+
Martina Bertsch, PhD
mbe404 at lulu.it.northwestern.edu
Thu Nov 20 00:40:02 CET 2003
The position restraints are molecule-based, therefore they must appear
inside the proper [ molecule_type ] subsection in the .top file. For
example, in your protein.top file, at the end of the listing of all
atoms, bonds, angles and dihedrals, you will find:
; Include position restraint file
after which if you are using, e.g., SPC water, you should also have:
; Include water topology
Also, at the end of the listing of atoms, bonds, etc. in the dppc.itp,
you will find:
Similarly, the ions.itp file contains a [ molecule_type ] section for
*each* of the separate ions, after which you should
insert the posres statement.
Of course, if you are using ifdef/endif, the *posre.itp will only be
included if the *mdp file defines the appropriate posres.
Martina Bertsch, Ph.D.
Feinberg School of Medicine
Molecular Pharmacology and Biological Chemistry
303 East Chicago Avenue
Chicago, IL 60611
Jodi Fangman wrote:
>Thank you for your help and the new ions.itp information. I used this new file
>and still recieved the error message No moleculetype K+(or NA+ or Na+) found.
>Do you have any idea why this is still happening? I included the part of my
>topology that I edited to see if there was anything wrong with it.
>; Include Position restraint file
>; Include water topology
>; Position restraint for each water oxygen
>[ position_restraints ]
>; i funct fcx fcy fcz
> 1 1 1000 1000 1000
>[ system ]
>UBIQUITIN in 100mM NaCl
>[ molecules ]
>; Compound #mols
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