[gmx-users] OPLS-AA and TIP4P errors

Ken Rotondi ksr at chemistry.umass.edu
Tue Nov 2 23:47:35 CET 2004

Hello All,
Just waiting for the results of the election to start rolling in...
I'm hitting my head against a wall here. I'm trying to use the 
following commands to generate a system consisting of a peptide, tip4p 
water and 2 Cl- ions to balance the charge.

pdb2gmx -f pep1.pdb -p pep1.top -o pep1.gro -water tip4p -ignh -ff 
genbox -cp pep1.gro -box 5 5 5 -o pep1box.gro
editconf -f pep1box.gro -o pep1boxc.gro -center 2.5 2.5 2.5 -c
genbox -cp pep1boxc.gro -cs tip4p.gro -o pep1boxcsol.gro -p pep1.top
grompp -v -f lbfgsmin.mdp -c pep1boxcsol.gro -p pep1.top -o pep1sol1.tpr
genion -s pep1sol1.tpr -o pep1sol1.gro -nn 2

Everything is fine to this point, however, since genion can't output a 
.top file (?!) I need to re-generate matched .gro/.top files, and 
attempt to do so with this command:
pdb2gmx -f pep1sol1.gro -o pep1sol1.gro -p pep1.top -i pep1sol1.itp -n 

Unfortunately this returns the following error:

Fatal error: Atom MW1 in residue HOH 1 not found in rtp entry with 3 
              while sorting atoms

I tried to hand edit the .top file to reflect the two lost waters that 
were replaced by Cl atoms, I checked the .gro and .top files, the end 
of the top file contained

[ molecules ]
; Compound        #mols
Protein             1
SOL              4045

I edited it to:

[ molecules ]
; Compound        #mols
Protein             1
SOL              4037
CL                     2

and ran:
grompp -v -f lbfgsmin.mdp -c pep1sol1.gro -p pep1sol1.top -o 

This returned a error of

Fatal error: No such moleculetype CL

I of course tried Cl,

Fatal error: No such moleculetype Cl

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.

Thanks (as always),


K.S. Rotondi Ph.D.
Research Fellow
The Gierasch Laboratory
Department of Biochemistry and Molecular Biology
University of Massachusetts-Amherst
Phone: 413-545-1250
Fax;      413-545-3291

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