[gmx-users] OPLS-AA and TIP4P errors

Dallas Warren dallas.warren at vcp.monash.edu.au
Wed Nov 3 02:23:59 CET 2004

>[ molecules ]
>; Compound        #mols
>Protein             1
>SOL              4045
>I edited it to:
>[ molecules ]
>; Compound        #mols
>Protein             1
>SOL              4037
>CL                     2

Firstly this should be SOL 4043, since you have only removed two water 
molecules to be replaced with the chloride.  The topology file contains 
number of molecules, not number of atoms.

>and ran:
>grompp -v -f lbfgsmin.mdp -c pep1sol1.gro -p pep1sol1.top -o pep1sol1.tpr
>This returned a error of
>Fatal error: No such moleculetype CL
>I of course tried Cl,
>Fatal error: No such moleculetype Cl

What is the atom/molecule name for chloride with the forcefield that you 
are using?

>What am I missing? Do I need to hand edit the rtp file to include 
>definitions for tip4p water? Forgive my ignorance, I'm just branching out 
>from gromos96 and SPC water.

Hope that helps some (note I haven't used OPLS-AA and TIP4P myself, so 
might be off base, but ....)

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
When the only tool you own is a hammer, every problem begins to resemble a nail.
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