[gmx-users] Charmm to gromacs conversion for lipids

[Venkat Reddy]

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?


On Thu, Nov 6, 2014 at 6:09 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036