Thank you Justin. On Sun, Mar 29, 2015 at 8:50 AM, Justin Lemkul <[email protected]> wrote:
> > > On 3/28/15 8:36 AM, Priya Das wrote: > >> This is the Paramchem generated file. >> >> * Toppar stream file generated by >> * CHARMM General Force Field (CGenFF) program version 0.9.7.1 beta >> * For use with CGenFF version 2b8 >> * >> >> read rtf card append >> * Topologies generated by >> * CHARMM General Force Field (CGenFF) program version 0.9.7.1 beta >> * using valence-based bond orders >> * >> 36 1 >> >> ! "penalty" is the highest penalty score of the associated parameters. >> ! Penalties lower than 10 indicate the analogy is fair; penalties between >> 10 >> ! and 50 mean some basic validation is recommended; penalties higher than >> ! 50 indicate poor analogy and mandate extensive validation/optimization. >> >> RESI Pose 0.000 ! param penalty= 117.000 ; charge penalty= 37.947 >> GROUP ! CHARGE CH_PENALTY >> ATOM N NG311 -0.299 ! 37.947 >> > > Check interactions with water here; the penalty is not that bad but you'll > want to check. > > > ATOM C1 CG311 -0.102 ! 9.362 >> ATOM C2 CG311 -0.102 ! 24.826 >> ATOM C3 CG311 -0.092 ! 12.017 >> ATOM C4 CG321 -0.181 ! 19.898 >> ATOM C5 CG321 -0.167 ! 18.342 >> ATOM C6 CG321 -0.165 ! 0.000 >> ATOM C7 CG311 -0.094 ! 17.735 >> ATOM C8 CG321 -0.183 ! 18.342 >> ATOM C9 CG321 -0.217 ! 15.714 >> ATOM H HGPAM1 0.345 ! 7.962 >> ATOM C10 CG321 -0.184 ! 18.342 >> ATOM C11 CG321 -0.181 ! 15.714 >> ATOM C12 CG331 -0.271 ! 0.030 >> ATOM C13 CG321 -0.180 ! 0.030 >> ATOM C14 CG321 -0.176 ! 0.030 >> ATOM C15 CG331 -0.271 ! 0.030 >> ATOM H2 HGA1 0.090 ! 1.100 >> ATOM H3 HGA1 0.090 ! 2.536 >> ATOM H4 HGA1 0.090 ! 0.000 >> ATOM H5 HGA2 0.090 ! 0.000 >> ATOM H6 HGA2 0.090 ! 0.000 >> ATOM H7 HGA2 0.090 ! 0.750 >> ATOM H8 HGA2 0.090 ! 0.750 >> ATOM H9 HGA2 0.090 ! 0.000 >> ATOM H10 HGA2 0.090 ! 0.000 >> ATOM H11 HGA1 0.090 ! 2.536 >> ATOM H12 HGA2 0.090 ! 0.750 >> ATOM H13 HGA2 0.090 ! 0.750 >> ATOM H14 HGA2 0.090 ! 0.000 >> ATOM H15 HGA2 0.090 ! 0.000 >> ATOM H16 HGA2 0.090 ! 0.750 >> ATOM H17 HGA2 0.090 ! 0.750 >> ATOM H18 HGA2 0.090 ! 0.000 >> ATOM H19 HGA2 0.090 ! 0.000 >> ATOM H20 HGA3 0.090 ! 0.000 >> ATOM H21 HGA3 0.090 ! 0.000 >> ATOM H22 HGA3 0.090 ! 0.000 >> ATOM H23 HGA2 0.090 ! 0.000 >> ATOM H24 HGA2 0.090 ! 0.000 >> ATOM H25 HGA2 0.090 ! 0.000 >> ATOM H26 HGA2 0.090 ! 0.000 >> ATOM H27 HGA3 0.090 ! 0.000 >> ATOM H28 HGA3 0.090 ! 0.000 >> ATOM H29 HGA3 0.090 ! 0.000 >> ! Bond order >> BOND N H ! 1 >> BOND N C2 ! 1 >> BOND N C7 ! 1 >> BOND C1 C4 ! 1 >> BOND C1 C3 ! 1 >> BOND C1 C2 ! 1 >> BOND C2 C5 ! 1 >> BOND C3 C13 ! 1 >> BOND C3 C6 ! 1 >> BOND C4 C8 ! 1 >> BOND C5 C9 ! 1 >> BOND C6 C9 ! 1 >> BOND C7 C8 ! 1 >> BOND C7 C10 ! 1 >> BOND C10 C11 ! 1 >> BOND C11 C12 ! 1 >> BOND C13 C14 ! 1 >> BOND C14 C15 ! 1 >> BOND C1 H2 ! 1 >> BOND C2 H3 ! 1 >> BOND C3 H4 ! 1 >> BOND C4 H5 ! 1 >> BOND C4 H6 ! 1 >> BOND C5 H7 ! 1 >> BOND C5 H8 ! 1 >> BOND C6 H9 ! 1 >> BOND C6 H10 ! 1 >> BOND C7 H11 ! 1 >> BOND C8 H12 ! 1 >> BOND C8 H13 ! 1 >> BOND C9 H14 ! 1 >> BOND C9 H15 ! 1 >> BOND C10 H16 ! 1 >> BOND C10 H17 ! 1 >> BOND C11 H18 ! 1 >> BOND C11 H19 ! 1 >> BOND C12 H20 ! 1 >> BOND C12 H21 ! 1 >> BOND C12 H22 ! 1 >> BOND C13 H23 ! 1 >> BOND C13 H24 ! 1 >> BOND C14 H25 ! 1 >> BOND C14 H26 ! 1 >> BOND C15 H27 ! 1 >> BOND C15 H28 ! 1 >> BOND C15 H29 ! 1 >> >> END >> >> read param card flex append >> * Parameters generated by analogy by >> * CHARMM General Force Field (CGenFF) program version 0.9.7.1 beta >> * >> >> ! Penalties lower than 10 indicate the analogy is fair; penalties between >> 10 >> ! and 50 mean some basic validation is recommended; penalties higher than >> ! 50 indicate poor analogy and mandate extensive validation/optimization. >> >> BONDS >> CG311 CG311 222.50 1.5000 ! PROT alkane update, adm jr., 3/2/92 >> CG311 CG321 222.50 1.5380 ! PROT alkane update, adm jr., 3/2/92 >> CG311 NG311 263.00 1.4740 ! Pose , from CG321 NG311, PENALTY= 4 >> CG311 HGA1 309.00 1.1110 ! PROT alkane update, adm jr., 3/2/92 >> CG321 CG321 222.50 1.5300 ! PROT alkane update, adm jr., 3/2/92 >> CG321 CG331 222.50 1.5280 ! PROT alkane update, adm jr., 3/2/92 >> CG321 HGA2 309.00 1.1110 ! PROT alkane update, adm jr., 3/2/92 >> CG331 HGA3 322.00 1.1110 ! PROT alkane update, adm jr., 3/2/92 >> NG311 HGPAM1 447.80 1.0190 ! AMINE aliphatic amines >> >> > Bonds are OK. > > > ANGLES >> CG311 CG311 CG311 53.35 111.00 8.00 2.56100 ! PROT alkane >> update, adm jr., 3/2/92 >> CG311 CG311 CG321 53.35 111.00 8.00 2.56100 ! PROT alkane >> update, adm jr., 3/2/92 >> CG311 CG311 NG311 43.70 112.20 ! Pose , from CG331 CG321 >> NG311, PENALTY= 5.5 >> CG311 CG311 HGA1 34.50 110.10 22.53 2.17900 ! PROT alkane >> update, adm jr., 3/2/92 >> CG321 CG311 CG321 58.35 113.50 11.16 2.56100 ! LIPID glycerol >> CG321 CG311 NG311 43.70 112.20 ! Pose , from CG331 CG321 >> NG311, PENALTY= 4.9 >> CG321 CG311 HGA1 34.50 110.10 22.53 2.17900 ! PROT alkane >> update, adm jr., 3/2/92 >> NG311 CG311 HGA1 32.40 109.50 50.00 2.13000 ! Pose , from >> NG311 CG321 HGA2, PENALTY= 4 >> CG311 CG321 CG321 58.35 113.50 11.16 2.56100 ! PROT alkanes >> CG311 CG321 HGA2 33.43 110.10 22.53 2.17900 ! PROT alkanes >> CG321 CG321 CG321 58.35 113.60 11.16 2.56100 ! PROT alkane >> update, adm jr., 3/2/92 >> CG321 CG321 CG331 58.00 115.00 8.00 2.56100 ! PROT alkane >> update, adm jr., 3/2/92 >> CG321 CG321 HGA2 26.50 110.10 22.53 2.17900 ! PROT alkane >> update, adm jr., 3/2/92 >> CG331 CG321 HGA2 34.60 110.10 22.53 2.17900 ! PROT alkane >> update, adm jr., 3/2/92 >> HGA2 CG321 HGA2 35.50 109.00 5.40 1.80200 ! PROT alkane >> update, adm jr., 3/2/92 >> CG321 CG331 HGA3 34.60 110.10 22.53 2.17900 ! PROT alkane >> update, adm jr., 3/2/92 >> HGA3 CG331 HGA3 35.50 108.40 5.40 1.80200 ! PROT alkane >> update, adm jr., 3/2/92 >> CG311 NG311 CG311 40.50 112.20 5.00 2.42170 ! Pose , from >> CG3AM1 NG311 CG3AM1, PENALTY= 35 >> > > This is the only really concerning entry among the angles. Verify with a > 3-point scan. > > > CG311 NG311 HGPAM1 35.00 111.00 ! Pose , from CG321 NG311 >> HGPAM1, PENALTY= 0.6 >> >> DIHEDRALS >> CG311 CG311 CG311 CG321 0.5000 4 180.00 ! NA bkb >> CG311 CG311 CG311 NG311 0.1400 3 0.00 ! Pose , from CG311 >> CG311 CG311 OG311, PENALTY= 38 >> CG311 CG311 CG311 HGA1 0.1950 3 0.00 ! NA, sugar >> CG321 CG311 CG311 CG321 0.5000 4 180.00 ! NA, sugar >> CG321 CG311 CG311 NG311 0.2000 3 180.00 ! Pose , from CG321 >> CG311 CG321 OG302, PENALTY= 37.5 >> CG321 CG311 CG311 HGA1 0.1950 3 0.00 ! NA, sugar >> NG311 CG311 CG311 HGA1 0.1600 3 0.00 ! Pose , from NG311 >> CG321 CG331 HGA3, PENALTY= 15 >> HGA1 CG311 CG311 HGA1 0.1950 3 0.00 ! NA, sugar >> CG311 CG311 CG321 CG321 0.2000 3 0.00 ! CHL1, Cholesterol >> reset to default by kevo >> CG311 CG311 CG321 HGA2 0.1950 3 0.00 ! NA, sugar >> CG321 CG311 CG321 CG321 0.2000 3 0.00 ! PROT alkane >> update, adm jr., 3/2/92 >> CG321 CG311 CG321 HGA2 0.1950 1 0.00 ! NA, sugar >> NG311 CG311 CG321 CG321 0.1950 3 0.00 ! Pose , from NG3P2 >> CG314 CG321 CG321, PENALTY= 37 >> NG311 CG311 CG321 HGA2 0.1600 3 0.00 ! Pose , from NG311 >> CG321 CG331 HGA3, PENALTY= 10 >> HGA1 CG311 CG321 CG321 0.1950 3 0.00 ! NA abasic nucleoside >> HGA1 CG311 CG321 HGA2 0.1950 3 0.00 ! NA, sugar >> CG311 CG311 NG311 CG311 2.5000 1 180.00 ! Pose , from NG311 >> CG321 NG311 CG2R61, PENALTY= 117 >> CG311 CG311 NG311 CG311 1.5000 2 0.00 ! Pose , from NG311 >> CG321 NG311 CG2R61, PENALTY= 117 >> CG311 CG311 NG311 CG311 0.5000 3 0.00 ! Pose , from NG311 >> CG321 NG311 CG2R61, PENALTY= 117 >> CG311 CG311 NG311 HGPAM1 0.1000 3 0.00 ! Pose , from CG331 >> CG321 NG311 HGP1, PENALTY= 7 >> CG321 CG311 NG311 CG311 2.5000 1 180.00 ! Pose , from NG311 >> CG321 NG311 CG2R61, PENALTY= 117 >> CG321 CG311 NG311 CG311 1.5000 2 0.00 ! Pose , from NG311 >> CG321 NG311 CG2R61, PENALTY= 117 >> CG321 CG311 NG311 CG311 0.5000 3 0.00 ! Pose , from NG311 >> CG321 NG311 CG2R61, PENALTY= 117 >> CG321 CG311 NG311 HGPAM1 0.1000 3 0.00 ! Pose , from CG331 >> CG321 NG311 HGP1, PENALTY= 6.4 >> HGA1 CG311 NG311 CG311 0.0000 3 180.00 ! Pose , from HGA2 >> CG321 NG311 CG2R61, PENALTY= 77.5 >> > > Dihedrals clearly need work, though by fixing one or two things, you may > dramatically bring down the penalties (and luckily the problems are largely > from the same couple of terms, not like you have to parametrize a bunch of > different dihedrals). The target data here would be QM energy values at > fixed 15-degree intervals of the target dihedrals, with everything else > free to relax. Since this is a ring system, a full scan of 360 degrees > won't be possible, but +/- 90 is a reasonable start. > > -Justin > > > HGA1 CG311 NG311 HGPAM1 0.0500 3 0.00 ! Pose , from HGA2 >> CG321 NG311 HGPAM1, PENALTY= 4 >> CG311 CG321 CG321 CG311 0.1950 3 0.00 ! PROT alkane >> update, adm jr., 3/2/92 >> CG311 CG321 CG321 CG321 0.5000 3 0.00 ! CARBOCY carbocyclic >> sugars >> CG311 CG321 CG321 CG321 0.5000 6 180.00 ! CARBOCY carbocyclic >> sugars >> CG311 CG321 CG321 CG331 0.1505 2 0.00 ! Pose , from CG321 >> CG321 CG321 CG331, PENALTY= 0.6 >> CG311 CG321 CG321 CG331 0.0813 3 180.00 ! Pose , from CG321 >> CG321 CG321 CG331, PENALTY= 0.6 >> CG311 CG321 CG321 CG331 0.1082 4 0.00 ! Pose , from CG321 >> CG321 CG321 CG331, PENALTY= 0.6 >> CG311 CG321 CG321 CG331 0.2039 5 0.00 ! Pose , from CG321 >> CG321 CG321 CG331, PENALTY= 0.6 >> CG311 CG321 CG321 HGA2 0.1950 3 0.00 ! NA abasic nucleoside >> CG321 CG321 CG321 HGA2 0.1950 3 0.00 ! LIPID alkanes >> CG331 CG321 CG321 HGA2 0.1800 3 0.00 ! LIPID alkane >> HGA2 CG321 CG321 HGA2 0.2200 3 0.00 ! LIPID alkanes >> CG321 CG321 CG331 HGA3 0.1600 3 0.00 ! PROT rotation >> barrier in Ethane (SF) >> HGA2 CG321 CG331 HGA3 0.1600 3 0.00 ! PROT rotation >> barrier in Ethane (SF) >> >> IMPROPERS >> >> END >> RETURN >> >> >> >> On Sat, Mar 28, 2015 at 5:51 PM, Justin Lemkul <[email protected]> wrote: >> >> >>> >>> On 3/28/15 7:05 AM, Priya Das wrote: >>> >>> I am sorry to bother again and again. I am new to it and still learning >>>> the basics. >>>> My molecule is a decahydroquinoline. The paramchem generated .str file >>>> is >>>> HERE >>>> <https://cgenff.paramchem.org/initguess/filedownload.php? >>>> file=20150328/Pose1.str> >>>> . >>>> >>>> >>> That file is not accessible. I'm not sure why there are high penalties >>> in >>> that molecule; it is very straightforward. >>> >>> I am following CGennFF tutorial and your instructions as HERE >>> >>>> <http://mackerell.umaryland.edu/~kenno/cgenff/program.html>. As >>>> penalties >>>> are there i need to use QM, but i am not able to run CHARMM simulations >>>> as >>>> CHARMM is not freely available. So tried to use this Toolkit >>>> <http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/>, but still in vain. >>>> >>>> >>>> Because neither CHARMM nor fftk do what you need to do. You need QM >>> software that is capable of doing geometry optimizations, angle and >>> dihedral scans, and vibrational analysis. We use Gaussian. If you don't >>> have access to that kind of software, you're not going to be able to >>> generate the target data you need, simply put. >>> >>> On the MM side, assuming you can generate the QM target data for >>> refinement, any package will work - CHARMM, GROMACS, etc. You don't >>> explicitly need CHARMM. You need something that can do energy >>> minimization >>> and single-point energy evaluations. >>> >>> >>> -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 >>> >>> [email protected] | (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 [email protected]. >>> >>> >> >> >> > -- > ================================================== > > 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 > > [email protected] | (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 [email protected]. > -- *Let us all join hands to save our " Mother Earth"* ------------------------------------------------------------------------ Regards, Priya Das Research Scholar Dept. of Computational Biology and Bioinformatics, University of Kerala -- 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 [email protected].
