[gmx-users] Charmm to gromacs conversion for lipids

[Venkat Reddy]

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

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