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 <jalem...@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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? 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