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outdated.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 <jalem...@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
jalem...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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