[gmx-users] Charmm to gromacs conversion for lipids

Venkat Reddy venkat4bt at gmail.com
Fri Nov 7 16:55:35 CET 2014 

Thank you Justin for the great help you have done, as you always been. I
will download the latest updated CHARMM36 files.

On Fri, Nov 7, 2014 at 6:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/7/14 12:30 AM, Venkat Reddy wrote:
>
>> Dear Justin,
>> Please check the atom section of "toppar_all36_lipid_cholesterol.str"
>> file
>> that I pasted below.
>>
>> * Toppar stream file for cholesterol.  Stream following reading of
>> * top_all36_lipid.rtf  and par_all36_lipid.rtf
>>
>> !reference
>> !Suits, F., Pitman, M., MacKerell, A.D., Jr., Feller, S.E. "Molecular
>> Level
>> !Organization of Saturated and Polyunsaturated Fatty Acids in a
>> !Phosphatidylcholine Bilayer Containing Cholesterol" Submitted
>> !for publication
>>
>>
> I see where the problem is.  Note that this file says "Submitted for
> publication," but it was actually published 10 years ago.  This stream file
> is outdated.  The CHL1 model I included in the CHARMM36 distribution is the
> current one, which uses CRL1 for C3 and a series of NBFIXes described in
> the 2012 paper by Lim et al. (full reference in forcefield.doc).
>
> You can get the latest, updated CHARMM36 force field files from
> http://mackerell.umaryland.edu/charmm_ff.shtml#charmm
>
> -Justin
>
>
>  read rtf card append
>> * cholesterol residues
>> *
>>
>> RESI CHL1          0.00  !cholesterol (name to avoid conflict with
>> choline)
>> ! atoms names correspond to the correct cholesterol nomenclature
>> GROUP
>> ATOM C3   CTL1     0.14
>> ATOM O3   OHL     -0.66
>> ATOM H3'  HOL      0.43
>> ATOM H3   HAL1     0.09
>> GROUP
>> ATOM C4   CTL2    -0.18
>> ATOM H4A  HAL2     0.09
>> ATOM H4B  HAL2     0.09
>> GROUP
>> ATOM C5   CEL1     0.00
>> ATOM C6   CEL1    -0.15
>> ATOM H6   HEL1     0.15
>> GROUP
>> ATOM C7   CTL2    -0.18
>> ATOM H7A  HAL2     0.09
>> ATOM H7B  HAL2     0.09
>> GROUP
>> ATOM C8   CTL1    -0.09
>> ATOM H8   HAL1     0.09
>> GROUP
>> ATOM C14  CTL1    -0.09
>> ATOM H14  HAL1     0.09
>> GROUP
>> ATOM C15  CTL2    -0.18
>> ATOM H15A HAL2     0.09
>> ATOM H15B HAL2     0.09
>> GROUP
>> ATOM C16  CTL2    -0.18
>> ATOM H16A HAL2     0.09
>> ATOM H16B HAL2     0.09
>> GROUP
>> ATOM C17  CTL1    -0.09
>> ATOM H17  HAL1     0.09
>> GROUP
>> ATOM C13  CTL1     0.00
>> GROUP
>> ATOM C18  CTL3    -0.27  !methyl at c13
>> ATOM H18A HAL3     0.09
>> ATOM H18B HAL3     0.09
>> ATOM H18C HAL3     0.09
>> GROUP
>> ATOM C12  CTL2    -0.18
>> ATOM H12A HAL2     0.09
>> ATOM H12B HAL2     0.09
>> GROUP
>> ATOM C11  CTL2    -0.18
>> ATOM H11A HAL2     0.09
>> ATOM H11B HAL2     0.09
>> GROUP
>> ATOM C9   CTL1    -0.09
>> ATOM H9   HAL1     0.09
>> GROUP
>> ATOM C10  CTL1     0.00
>> GROUP
>> ATOM C19  CTL3    -0.27  !methyl at c10
>> ATOM H19A HAL3     0.09
>> ATOM H19B HAL3     0.09
>> ATOM H19C HAL3     0.09
>> GROUP
>> ATOM C1   CTL2    -0.18
>> ATOM H1A  HAL2     0.09
>> ATOM H1B  HAL2     0.09
>> GROUP
>> ATOM C2   CTL2    -0.18
>> ATOM H2A  HAL2     0.09
>> ATOM H2B  HAL2     0.09
>> GROUP
>> ATOM C20  CTL2    -0.09
>> ATOM H20  HAL2     0.09
>> GROUP
>> ATOM C21  CTL3    -0.27
>> ATOM H21A HAL3     0.09
>> ATOM H21B HAL3     0.09
>> ATOM H21C HAL3     0.09
>> GROUP
>> ATOM C22  CTL2    -0.18
>> ATOM H22A HAL2     0.09
>> ATOM H22B HAL2     0.09
>> GROUP
>> ATOM C23  CTL2    -0.18
>> ATOM H23A HAL2     0.09
>> ATOM H23B HAL2     0.09
>> GROUP
>> ATOM C24  CTL2    -0.18  !beyond this nomenclature may not be correct
>> ATOM H24A HAL2     0.09
>> ATOM H24B HAL2     0.09
>> GROUP
>> ATOM C25  CTL1    -0.09  !c25
>> ATOM H25  HAL1     0.09
>> GROUP
>> ATOM C26  CTL3    -0.27  !terminal methyl, c26
>> ATOM H26A HAL3     0.09
>> ATOM H26B HAL3     0.09
>> ATOM H26C HAL3     0.09
>> GROUP
>> ATOM C27  CTL3    -0.27  !terminal methyl, c27
>> ATOM H27A HAL3     0.09
>> ATOM H27B HAL3     0.09
>> ATOM H27C HAL3     0.09
>>
>> On Thu, Nov 6, 2014 at 7:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 11/6/14 8:38 AM, Venkat Reddy wrote:
>>>
>>>  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.
>>>>
>>>>
>>>>  Thanks, I will fix that.
>>>
>>>   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.
>>>>
>>>>
>>>>  Which residue are you looking at?  There is no C3 atom with type CTL1
>>> in
>>> that stream file.  In any case, CG311 and CTL1 have identical parameters
>>> (see ffnonbonded.itp) since CG311 is used for CGenFF model compounds,
>>> which
>>> in the case of lipids, were just ported over and given unique types.
>>> Anything with a "G" as the second letter in the atom type is from CGenFF,
>>> indicating "general" to differentiate them from the main CHARMM types.
>>>
>>>
>>> -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

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