[gmx-users] Query- Ligand parametrization
Priya Das
priyadas001 at gmail.com
Tue Mar 31 11:15:12 CEST 2015
Thank you Justin.
On Sun, Mar 29, 2015 at 8:50 AM, Justin Lemkul <jalemkul at vt.edu> 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 <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
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
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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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
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>
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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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