[gmx-users] Problem: pdb2gmx with a more complex system

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 27 04:04:17 CEST 2012

Jernej Zidar wrote:
> Hi.
>   I'm trying to import a PDB containing the following components to
> Gromacs using pdb2gmx:
> - polymer (1 molecule composed of 5 residues)
> - lipids (cholesterol-37 molecules and sphingomyelin-78 molecules)
> - water (2297 molecules)
>   The problem I have is that for some strange reason pdb2gmx does not
> recognize the lipid part as being composed of 112 molecules, but
> rather just as one molecule.
>   If I attempt to manually correct this to 112, grompp complains about
> the system containing 1345900 atoms (total number of lipid atoms
> 11954*112 molecules+161 from the polymer bit+6891 from water) instead
> of 19006 atoms (161 from the polymer bit, 11954 from the lipids, 6891
> from water).

It sounds like you're confusing "molecule" with "moleculetype."  In Gromacs, a 
moleculetype need not contain a single chemical molecule; it can contain any 
combination of atoms.  If you tell grompp that there are 112 copies of the 
moleculetype, then you get the behavior you're seeing.

When dealing with a complex system like this one, it is often far easier to:

1. Create a coordinate file of each individual molecule type (true molecule, 
that is your polymer, cholesterol, and sphingomyelin)
2. Run pdb2gmx on each of these to obtain an individual molecule topology
3. Remove the unnecessary #include statements and directives from the resulting 
molecule .top files to convert them to .itp
4. Create your own topology that simply uses #include statements
5. If you have alternating molecules in the coordinate file, re-order it so it 
has each molecular species in blocks for far easier topology handling

Such a procedure creates a .top that is less redundant and more clear topology.

>   Questions:
> a) Why are the water molecules properly recognized? The only thing I
> had to do was to use some sed commands to change the segment name from
> "bulk" to SOL and the atomtypes from TIP3 (OH2, H1, H2) to SPC (OW,
> HW1, HW2).

Atom naming must match whatever Gromacs conventions are in place.

> b) I used CHARMM to generate the lipid bilayer. The membrane building
> process occurs in two stages so the residues in the resulting bilayers
> are arranged in this order: cholesterol, sphingomyelin, cholesterol,
> sphingomyelin. Could this be the cause?
>   Why aren't the lipid residues recognized as separate molecules?

Again I think you are confusing the terminology and convention here.


>   The lipid molecules are defined as separate molecules in the joined
> charmm36cgenff forcefield, where I used the existing lipid molecules
> in lipids.rtp as a template to add my own molecules.
>   I should emphasize the all the residues/molecules work perfectly
> within CHARMM, but then again CHARMM has a different modus operandi.
> Thanks in advance for any help,
> Jernej Zidar


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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