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 <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 > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.