[gmx-users] Charmm to gromacs conversion for lipids

[Justin Lemkul]

On 11/6/14 12:45 AM, Venkat Reddy wrote:
> Dear Justin,
> Thanks for the update. But unfortunately I couldn't find the parameters for
> cholesteryl oleate. So, I tried to convert again the parameters from CHARMM
> to GROMACS using these updated files:
>
> ./cgenff_charmm2gmx.py CHL1 CE-1.mol2 top_chol_ester.rtf
> /usr/local/gromacs/share/gromacs/top/charmm36-nov2014.ff
>
> Here I am getting an error like,
>
> Traceback (most recent call last):
>    File "./cgenff_charmm2gmx.py", line 778, in <module>
>      atomtypes = read_gmx_atomtypes(atomtypes_filename)
>    File "./cgenff_charmm2gmx.py", line 71, in read_gmx_atomtypes
>      var = [entry[0],entry[1]]
> IndexError: list index out of range
>
> If I use the charmm36 files uploaded in March 2014, Its not throwing any
> error. Is there something wrong in the updated files?
>

Possibly.  There is a blank line at the end of atomtypes.atp - does the error go 
away if you delete this blank line?

Also note that you don't need to re-convert your topology; what I was suggesting 
was that the new force field files cover more parameters for lipids, so if the 
needed dihedral is present (I can't actually say because you only provided two 
of the atom types) then your topology should work without any changes.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================