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 <jalem...@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 is outdated.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 <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. >>> >>> >> >> >> > -- > ================================================== > > 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.