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
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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
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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