[gmx-users] Charmm to gromacs conversion for lipids

[Venkat Reddy]

Thank you Justin for the tip. I have given .rtf file as input and the
script has generated me the desired output .itp file. The command I used is
as shown below.

./cgenff_charmm2gmx.py CHL1 CE-1.mol2 top_chol_ester.rtf
/usr/local/gromacs/share/gromacs/top/charmm36.ff


Thank you very much Justin for the help.

On Wed, Nov 5, 2014 at 6:05 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/5/14 7:33 AM, Venkat Reddy wrote:
>
>> Dear Justin,
>> My lipid is cholesteryl oleate (CO). Since there are CHARMM36 parameters
>> available for cholesterol and oleate chain in POPC, I have clubbed both
>> together to generate the topology for CO (rtf file). Now I want to convert
>> this rtf to itp file. is there any shortcut to accomplish this task?
>>
>>
> In theory, our conversion script should handle that, because all the .str
> files are are .rtf and .prm entries, so if you don't have any new
> parameters, it can probably convert the .rtf itself.  Never tried it, but
> you can probably make it work.  Error messages are pretty descriptive in
> case of any issues.
>
> -Justin
>
>
>  On Wed, Nov 5, 2014 at 5:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 11/5/14 7:03 AM, Venkat Reddy wrote:
>>>
>>>  Thank you Joao for the quick reply. My system has single lipid molecule
>>>> and
>>>> I have pre- calculated charge information for every atom in the lipid. I
>>>> have edited charges on individual atoms apart from atom types.
>>>> By the way, Previous studies have reported a topology for same lipid but
>>>> in
>>>> NAMD convention. Is there any other tool to convert NAMD to GROMACS
>>>> compatible format?
>>>>
>>>>
>>>>  You have to be careful here.  I would not use CGenFF for lipids, but
>>> for
>>> reasons different than what Joao was saying.  As is cautioned in the
>>> CGenFF
>>> description, you shouldn't use it for molecules for which a highly tuned
>>> biomolecular force field already covers much of, if not all, of the
>>> chemical space.  The CHARMM36 lipid force field is highly optimized and
>>> performs very well.  CGenFF, by its nature, is generalized.  With
>>> generalization and increased transferability comes a decrease in
>>> accuracy.
>>> Coupling charges calculated by a different method (is it compatible with
>>> what CHARMM normally requires, and are those charges tuned against the LJ
>>> parameters of the atom types to give reasonable intermolecular and
>>> water-water interactions?) with somewhat less accurate atom types and
>>> bonded parameters will probably lead to a poor result because you've got
>>> a
>>> hodge-podge of a topology.
>>>
>>> What is this lipid that you're trying to parametrize?  Are its functional
>>> groups covered by the existing parameters in the CHARMM36 lipid force
>>> field?  If they are, you should absolutely be using those parameters
>>> (charges, atom types, and bonded parameters).  Even small inaccuracies or
>>> imbalances can have a huge impact, especially on lipids, which are very
>>> sensitive.
>>>
>>> -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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>>
>>
>>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036