[gmx-users] Charmm to gromacs conversion for lipids

[Venkat Reddy]

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.

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.



On Thu, Nov 6, 2014 at 6:21 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

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