[gmx-users] Charmm to gromacs conversion for lipids

Justin Lemkul jalemkul at vt.edu
Thu Nov 6 14:46:37 CET 2014

On 11/6/14 8:38 AM, Venkat Reddy wrote:
> Dear Justin,
> Yes, the problem is with the blank line at the end of atomtypes.atp. Now
> its working fine. I have added the missing dihedral types from other
> sources.

Thanks, I will fix that.

> I have compared the cholesterol CHARMM parameters that are converted to
> gromacs format and original parameters from
> "toppar_all36_lipid_cholesterol.str" file available in CHARMM website. I
> found some variations in the atom types.
> For eg., The atom type of  C3 atom from sterol ring in cholesterol is CTL1
> in CHARMM whereas it is CG311 in charmm36-Nov2014.ff.

Which residue are you looking at?  There is no C3 atom with type CTL1 in that 
stream file.  In any case, CG311 and CTL1 have identical parameters (see 
ffnonbonded.itp) since CG311 is used for CGenFF model compounds, which in the 
case of lipids, were just ported over and given unique types.  Anything with a 
"G" as the second letter in the atom type is from CGenFF, indicating "general" 
to differentiate them from the main CHARMM types.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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