[gmx-users] How to reduce the penalty of small molecule from CGenFF
Rolly Ng
rollyng at gmail.com
Sun Mar 29 07:30:10 CEST 2020
Hello Justin,
Thank you and yes. I went to the paper and it shows the steps for
optimization.
However, I have the following problems as I tried to follow the tutorial on
CGenFF page, http://mackerell.umaryland.edu/~kenno/cgenff/download.php#tutor
(1) what are these parameters in water_constr.inp? what values should I use
in my case?
if @stage eq 4 echo ######## USING MP2 GEOMETRY!!! ########
echo QM dipole (Debye)
echo mp2/6-31g*: X= -3.1938 Y= 1.2595 Z= 0.0011 Tot=
3.4332
echo hf/6-31g*: X= -3.4411 Y= 1.3570 Z= 0.0012 Tot=
3.6990
(2) How can I get the correct value for the IC table for surface of
interest? I suppose H2O molecules are placed one at a time to the C and N
atoms of my molecule but where to place the dummy?
generate dum first none last none setup warn noangle nodihedral
join @residue dum renumber
!preparation of IC table for surface of interest
ic edit
dihe 1 N2 1 C1 1 H1 3 dum 0.0
dihe 1 C1 1 H1 3 dum 4 dum 0.0
dihe 4 dum 3 dum 1 H1 2 oh2 180.0
end
ic fill preserve
ic edit
dihe 3 dum 1 H1 2 oh2 2 h1 90.0
dihe 3 dum 1 H1 2 oh2 2 h2 -90.0
bond 1 H1 3 dum 1.
bond 3 dum 4 dum 1.
bond 1 H1 2 oh2 @d !varied
bond 2 oh2 2 h1 0.9572
bond 2 oh2 2 h2 0.9572
angl 1 C1 1 H1 3 dum 90.0
angl 1 H1 3 dum 4 dum 90.0
angl 3 dum 1 H1 2 oh2 90.0
angl 1 H1 2 oh2 2 h1 127.74
angl 1 H1 2 oh2 2 h2 127.74
end
How can I know the bond, angle and dihedral without a GUI show these
parameters?
Thanks for your patient.
Regards,
Rolly
On Thu, Mar 26, 2020 at 2:38 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 3/25/20 12:52 PM, Rolly Ng wrote:
> > Dear Gromacs Users,
> >
> >
> >
> > I am new to Gromacs and I followed the Protein-Ligand tutorial on the
> > following webpage,
> >
> > http://www.mdtutorials.com/gmx/complex/02_topology.html
> >
> >
> >
> > It works for the example JZ4 but as I changed to another molecule, the
> str
> > file produced by the CGenFF server states very high penalty 84.5
> >
> >
> >
> > Please have a look at my mol2 input and str output below. Your advises
> are
> > much appreciated!
> >
> >
>
> Have you read the CGenFF papers? The original 2010 JCC article is
> basically a tutorial and review of the parametrization theory.
>
> -Justin
>
> >
> > Thank you,
> >
> > Rolly
> >
> >
> >
> > @<TRIPOS>MOLECULE
> >
> > MF8
> >
> > 20 19 0 0 0
> >
> > SMALL
> >
> > GASTEIGER
> >
> >
> >
> > @<TRIPOS>ATOM
> >
> > 1 N08 19.3800 -17.4900 12.2190 N.pl3 1 MF8
> -0.2888
> >
> > 2 C07 19.5160 -18.4740 11.4320 C.cat 1 MF8
> 0.3855
> >
> > 3 N06 20.0120 -18.2750 10.1980 N.pl3 1 MF8
> -0.1861
> >
> > 4 N09 19.1990 -19.7060 11.8570 N.pl3 1 MF8
> -0.1293
> >
> > 5 C01 18.6460 -20.7310 8.7020 C.3 1 MF8
> 0.0558
> >
> > 6 N02 19.3290 -19.4990 8.3110 N.pl3 1 MF8
> -0.2675
> >
> > 7 N05 18.6660 -17.3520 8.6680 N.pl3 1 MF8
> -0.1291
> >
> > 8 C04 19.3130 -18.3670 9.0550 C.cat 1 MF8
> 0.3896
> >
> > 9 C03 20.0370 -19.6170 7.0360 C.3 1 MF8
> 0.0558
> >
> > 10 H 19.6101 -16.5820 11.9161 H 1 MF8
> 0.2547
> >
> > 11 H 19.0443 -17.6336 13.1333 H 1 MF8
> 0.2547
> >
> > 12 H 20.9660 -18.0428 10.1266 H 1 MF8
> 0.2707
> >
> > 13 H 19.3013 -20.4766 11.2529 H 1 MF8
> 0.3062
> >
> > 14 H 18.8055 -21.4799 7.9546 H 1 MF8
> 0.0619
> >
> > 15 H 17.5973 -20.5420 8.7994 H 1 MF8
> 0.0619
> >
> > 16 H 19.0353 -21.0729 9.6382 H 1 MF8
> 0.0619
> >
> > 17 H 18.1443 -17.3894 7.8339 H 1 MF8
> 0.3062
> >
> > 18 H 19.9010 -20.6026 6.6424 H 1 MF8
> 0.0619
> >
> > 19 H 21.0802 -19.4349 7.1891 H 1 MF8
> 0.0619
> >
> > 20 H 19.6476 -18.8997 6.3441 H 1 MF8
> 0.0619
> >
> > @<TRIPOS>BOND
> >
> > 1 1 2 1
> >
> > 2 1 10 1
> >
> > 3 1 11 1
> >
> > 4 2 3 1
> >
> > 5 2 4 2
> >
> > 6 3 8 1
> >
> > 7 3 12 1
> >
> > 8 4 13 1
> >
> > 9 5 6 1
> >
> > 10 5 14 1
> >
> > 11 5 15 1
> >
> > 12 5 16 1
> >
> > 13 6 9 1
> >
> > 14 6 8 1
> >
> > 15 7 8 2
> >
> > 16 7 17 1
> >
> > 17 9 18 1
> >
> > 18 9 19 1
> >
> > 19 9 20 1
> >
> >
> >
> >
> >
> > * Toppar stream file generated by
> >
> > * CHARMM General Force Field (CGenFF) program version 1.0.0
> >
> > * For use with CGenFF version 3.0.1
> >
> > *
> >
> >
> >
> > read rtf card append
> >
> > * Topologies generated by
> >
> > * CHARMM General Force Field (CGenFF) program version 1.0.0
> >
> > *
> >
> > 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 MF8 0.000 ! param penalty= 84.500 ; charge penalty=
> 12.315
> >
> > GROUP ! CHARGE CH_PENALTY
> >
> > ATOM N08 NG321 -0.603 ! 2.500
> >
> > ATOM C07 CG2N1 0.547 ! 5.000
> >
> > ATOM N06 NG311 -0.430 ! 6.533
> >
> > ATOM N09 NG2D1 -0.907 ! 2.500
> >
> > ATOM C01 CG331 -0.141 ! 9.593
> >
> > ATOM N02 NG301 -0.371 ! 12.315
> >
> > ATOM N05 NG2D1 -0.861 ! 4.101
> >
> > ATOM C04 CG2N1 0.609 ! 10.954
> >
> > ATOM C03 CG331 -0.141 ! 9.593
> >
> > ATOM H1 HGPAM2 0.330 ! 0.000
> >
> > ATOM H2 HGPAM2 0.330 ! 0.000
> >
> > ATOM H3 HGPAM1 0.360 ! 0.090
> >
> > ATOM H4 HGP1 0.369 ! 0.000
> >
> > ATOM H5 HGA3 0.090 ! 2.518
> >
> > ATOM H6 HGA3 0.090 ! 2.518
> >
> > ATOM H7 HGA3 0.090 ! 2.518
> >
> > ATOM H8 HGP1 0.369 ! 0.030
> >
> > ATOM H9 HGA3 0.090 ! 2.518
> >
> > ATOM H10 HGA3 0.090 ! 2.518
> >
> > ATOM H11 HGA3 0.090 ! 2.518
> >
> >
> >
> > BOND N08 C07
> >
> > BOND N08 H1
> >
> > BOND N08 H2
> >
> > BOND C07 N06
> >
> > BOND C07 N09
> >
> > BOND N06 C04
> >
> > BOND N06 H3
> >
> > BOND N09 H4
> >
> > BOND C01 N02
> >
> > BOND C01 H5
> >
> > BOND C01 H6
> >
> > BOND C01 H7
> >
> > BOND N02 C03
> >
> > BOND N02 C04
> >
> > BOND N05 C04
> >
> > BOND N05 H8
> >
> > BOND C03 H9
> >
> > BOND C03 H10
> >
> > BOND C03 H11
> >
> > IMPR C07 N09 N06 N08
> >
> > IMPR C04 N05 N02 N06
> >
> >
> >
> > END
> >
> >
> >
> > read param card flex append
> >
> > * Parameters generated by analogy by
> >
> > * CHARMM General Force Field (CGenFF) program version 1.0.0
> >
> > *
> >
> >
> >
> > ! 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
> >
> > CG2N1 NG301 500.00 1.4400 ! MF8 , from CG2N1 NG311, penalty= 5
> >
> > CG331 NG301 255.00 1.4630 ! MF8 , from CG331 NG311, penalty= 5
> >
> >
> >
> > ANGLES
> >
> > NG2D1 CG2N1 NG301 50.00 125.00 ! MF8 , from NG2D1 CG2N1 NG311,
> > penalty= 0.6
> >
> > NG301 CG2N1 NG311 50.00 113.00 ! MF8 , from NG311 CG2N1 NG321,
> > penalty= 1.8
> >
> > NG301 CG331 HGA3 30.50 109.70 50.00 2.14000 ! MF8 , from
> NG311
> > CG331 HGA3, penalty= 0.6
> >
> > CG2N1 NG301 CG331 43.00 106.00 ! MF8 , from CG2N1 NG311 CG331,
> > penalty= 5
> >
> > CG331 NG301 CG331 53.00 110.90 ! MF8 , from CG3AM0 NG301 CG3AM0,
> > penalty= 36.6
> >
> > CG2N1 NG311 CG2N1 40.00 109.00 ! MF8 , from CG2R61 NG311 CG2R61,
> > penalty= 46
> >
> >
> >
> > DIHEDRALS
> >
> > NG301 CG2N1 NG2D1 HGP1 5.2000 2 180.00 ! MF8 , from NG311
> CG2N1
> > NG2D1 HGP1, penalty= 0.6
> >
> > NG2D1 CG2N1 NG301 CG331 0.5000 2 180.00 ! MF8 , from NG2D1
> CG2N1
> > NG311 CG331, penalty= 5
> >
> > NG311 CG2N1 NG301 CG331 0.5000 2 180.00 ! MF8 , from NG321
> CG2N1
> > NG311 CG331, penalty= 6.2
> >
> > NG2D1 CG2N1 NG311 CG2N1 0.5000 2 180.00 ! MF8 , from NG2D1
> CG2N1
> > NG311 CG331, penalty= 69.9
> >
> > NG301 CG2N1 NG311 CG2N1 0.5000 2 180.00 ! MF8 , from NG321
> CG2N1
> > NG311 CG331, penalty= 71.7
> >
> > NG301 CG2N1 NG311 HGPAM1 2.8000 2 180.00 ! MF8 , from NG321
> CG2N1
> > NG311 HGPAM1, penalty= 1.8
> >
> > NG321 CG2N1 NG311 CG2N1 0.5000 2 180.00 ! MF8 , from NG321
> CG2N1
> > NG311 CG331, penalty= 69.9
> >
> > HGA3 CG331 NG301 CG2N1 0.0000 3 180.00 ! MF8 , from HGA3
> CG331
> > NG311 CG2N1, penalty= 5
> >
> > HGA3 CG331 NG301 CG331 0.0000 3 180.00 ! MF8 , from HGA2
> CG321
> > NG311 CG2R61, penalty= 84.5
> >
> >
> >
> > IMPROPERS
> >
> > CG2N1 NG2D1 NG301 NG311 85.0000 0 0.00 ! MF8 , from CG2N1
> NG2D1
> > NG311 NG321, penalty= 1.5
> >
> >
> >
> > END
> >
> > RETURN
> >
> >
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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