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

Mark Abraham Mark.Abraham at anu.edu.au
Tue Mar 27 04:06:05 CEST 2012

On 27/03/2012 12:57 PM, 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).

For the purposes of [system], a molecule is the contents of a 
[moleculetype]. So an arbitrary change to a number of molecules will 
have the effect you observe.

>    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).
> 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?

All this depends on the form of the coordinate file and how pdb2gmx has 
been instructed to interpret chain IDs and/or TER cards. Check out 
pdb2gmx -h


>    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

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