[gmx-users] Query- Ligand parametrization
Priya Das
priyadas001 at gmail.com
Sat Mar 28 13:36:37 CET 2015
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
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
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
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
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 <jalemkul at vt.edu> 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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--
*Let us all join hands to save our " Mother Earth"*
------------------------------------------------------------------------
Regards,
Priya Das
Research Scholar
Dept. of Computational Biology and Bioinformatics,
University of Kerala
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