[gmx-users] Charmm to gromacs conversion for lipids

Wed Nov 5 16:23:46 CET 2014

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?

Thank you for your valuable time.

On Wed, Nov 5, 2014 at 6:16 PM, Venkat Reddy <venkat4bt at gmail.com> wrote:

> 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
>>>>
>>>> ==================================================
>>>> --
>>>> Gromacs Users mailing list
>>>>
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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
>>
>> * Please search the archive at http://www.gromacs.org/
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>
>
>
> --
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
>

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