[gmx-users] Charmm to gromacs conversion for lipids

[Justin Lemkul]

On 11/5/14 10:23 AM, Venkat Reddy wrote:
> Dear Justin,
> While processing the lipid file using grompp, there was an error:
>
> ERROR 1 [file chl1.itp, line 938]:
>    No default Proper Dih. types
>
>
> ERROR 2 [file chl1.itp, line 939]:
>    No default Proper Dih. types
>
>
> ERROR 3 [file chl1.itp, line 940]:
>    No default Proper Dih. types
>
>
> ERROR 4 [file chl1.itp, line 942]:
>    No default Proper Dih. types
>
>
> ERROR 5 [file chl1.itp, line 944]:
>    No default Proper Dih. types
>
>
> ERROR 6 [file chl1.itp, line 945]:
>    No default Proper Dih. types
>
>
> ERROR 7 [file chl1.itp, line 946]:
>    No default Proper Dih. types
>
>
> ERROR 8 [file chl1.itp, line 947]:
>    No default Proper Dih. types
>
>
> ERROR 9 [file chl1.itp, line 948]:
>    No default Proper Dih. types
>
>
> ERROR 10 [file chl1.itp, line 949]:
>    No default Proper Dih. types
>
>
> ERROR 11 [file chl1.itp, line 956]:
>    No default Proper Dih. types
>
>
> ERROR 12 [file chl1.itp, line 959]:
>    No default Proper Dih. types
>
>
> I quickly went through the itp file and found atom types CEL1 and CTL1 as a
> part of dihedral are troubling. I have checked the parent rtf file for the
> dihedral definition of these atoms. The dihedral was defined as
>
>   C3 C4 C5 C10 1.5367 111.70 54.04 115.09 1.5304
>
> How to mention this information in ffbonded.itp?
>

Parameters should be specified by atom type, not atom name.  Regardless, you can 
always add parameters to [dihedraltypes] in ffbonded.itp after unit conversion. 
  Try the latest CHARMM36 force field files, which I just uploaded today:

http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

I added a bunch of lipids and associated parameters that people had asked for. 
Maybe what you need is already included there.

-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

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