[gmx-users] GROMPP replaces lipid atom coordinates with these of water molecules

Christian Blouin cblouin at cs.dal.ca
Mon Jul 23 15:54:35 CEST 2012


       I have been running a simple simulation where I replace 150
water molecules in a waterbox with a lipid called DPC to create
micelles. This simulation is working fine and I'm getting decent
micelles fairly quickly. I am now trying to do the same, but with a
small peptide in the simulation box. I think that grompp is using
water molecules coordinates to locate the DPC, making non-sensical
molecules. Why is grompp doing this in the simulation with the peptide
and not without is what stomps me. Here follow more details about my
system and errors:

A PDB of this atomic mess can be found here:

I've been working on this for a while now, with no success. Can anyone
point me in the right direction?




Here are the command lines that I use:

pdb2gmx -f 2LOU.pdb -o protein.gro -i ./include.itp -p protein.top -ignh
editconf -f protein.gro -o protein-PBC.gro -bt dodecahedron -d 1.0
genbox -cp protein-PBC.gro -cs spc216.gro -ci dpc -nmol 150 -p
protein.top -o protein-water.gro
python edittop.py (this python script adjust the protein.top file for
the right count of DPC and adds the include statement for DPC).

grompp -f minim.mdp -c protein-water.gro -p protein.top -o
protein-water.tpr -maxwarn 4

The last grompp command generates the following warning:
Warning: atom name 665 in protein.top and protein-water.gro does not
match (OW - C1)
Warning: atom name 666 in protein.top and protein-water.gro does not
match (HW1 - C2)
Warning: atom name 667 in protein.top and protein-water.gro does not
match (HW2 - C3)
WARNING 1 [file protein.top, line 4194]:
  6900 non-matching atom names
  atom names from protein.top will be used
  atom names from protein-water.gro will be ignored

If I extract a PDB from the tpr file, the system looks fine except for
all of the DPC atoms are now crammed into a rectangular box at the
edge of my PBC. In fact, it looks like the coordinates used for the
DPC molecules are these of water molecules that got reassigned to the
lipids residues.

The topology and gro file (if this helps):

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