[gmx-users] No molecule type K+

[Martina Bertsch, PhD]

Dear Jodi,

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
#ifdef POSRES
#include "posre.itp"
#endif

after which if you are using, e.g., SPC water, you should also have:

; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

Also, at the end of the listing of atoms, bonds, etc. in the dppc.itp, 
you will find:

#ifdef POSRES_LIPID
#include "lipid_posre.itp"
#endif

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.

Best regards,

Martina Bertsch, Ph.D.
Northwestern University
Feinberg School of Medicine
Molecular Pharmacology and Biological Chemistry
303 East Chicago Avenue
Chicago, IL 60611

Jodi Fangman wrote:

>David
>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
>#ifdef POSRES
>#include "posre.itp"
>#endif
>
>; Include water topology
>#include "ions.itp"
>#ifdef FLEX_SPC
>#include "flexspc.itp"
>#else
>#include "spc.itp"
>#endif
>
>#ifdef POSRES_WATER
>; Position restraint for each water oxygen
>[ position_restraints ]
>;  i funct       fcx        fcy        fcz
>   1    1       1000       1000       1000
>#endif
>
>[ system ]
>; Name
>UBIQUITIN in 100mM NaCl
>[ molecules ]
>; Compound        #mols
>Protein             1
>SOL              4513
>NA+                 4
>CL-                 4
>
>Thank you
>Jodi
>
>