[gmx-users] Pre-equilibrated CHARMM lipid bilayers

Peter C. Lai pcl at uab.edu
Thu Dec 20 10:25:02 CET 2012

I don't know.

Parachem outputs stuff like this (CHARMM toppar format):

(propionic acid, C3H2O5)

RESI PROA         -1.00 
ATOM  C2  CG321   -0.28 
ATOM  C1  CG2O3    0.62 
ATOM  H21 HGA2     0.09 
ATOM  H22 HGA2     0.09                       
ATOM  O1  OG2D2   -0.76 
ATOM  O2  OG2D2   -0.76 
ATOM  C3  CG331   -0.27 
ATOM  H31 HGA3     0.09
ATOM  H32 HGA3     0.09
ATOM  H33 HGA3     0.09

BOND C1 C2  C2 C3  C1 O1
BOND C2 H21 C2 H22
BOND C3 H31 C3 H32 C3 H33
IMPR C1 O2 O1 C2

which you can easily write a script to convert to .rtp (or just convert by
hand) but it'd be more complicated to create an entire .itp from this
format; pdb2gmx will do it if you convert this to .rtp though. I also
frequently encounter ligands that don't have hydrogens too, so that's why
I would write a .hdb entry if necessary.

(As a side note, Gromacs shouldn't use charge groups when using 
all-atom charmm forcefields.)

On 2012-12-20 09:27:12AM +0100, Albert wrote:
> On 12/20/2012 09:13 AM, pcl wrote:
> > Well what works for me is I convert cgenff and merge it with charmm36 (you only have to do this once per cgenff version), then I have paramchem generate cgenff charges for the ligand. Then I convert the output of paramchem (charges) to .rtp format. I also have to create .hdb entries. Paramchem may also generate additional cgenff atom interactions (dihedrals or impropers) that may not exist by default, I usually convert and add those to forcefield's .itp files. Then pdb2gmx will work on the ligand pdb.
> but isn't there is a script to do so in Gromacs webiste, which can 
> convert the output from parachem into Gromacs .itp format? although I 
> didn't try it hard, because I don't find any documentation to use it 
> correctly.....
> -- 
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