Re: [gmx-users] How to reduce the penalty of small molecule from CGenFF
On 3/29/20 1:29 AM, Rolly Ng wrote: 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=-3.1938Y= 1.2595Z= 0.0011 Tot= 3.4332 echo hf/6-31g*: X=-3.4411Y= 1.3570Z= 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. If you have questions about CHARMM, you should use the CHARMM forum. -Justin -- == 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? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to reduce the penalty of small molecule from CGenFF
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=-3.1938Y= 1.2595Z= 0.0011 Tot= 3.4332 echo hf/6-31g*: X=-3.4411Y= 1.3570Z= 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 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 > > > > > > > > @MOLECULE > > > > MF8 > > > > 20 19 0 0 0 > > > > SMALL > > > > GASTEIGER > > > > > > > > @ATOM > > > >1 N0819.3800 -17.4900 12.2190 N.pl3 1 MF8 > -0.2888 > > > >2 C0719.5160 -18.4740 11.4320 C.cat 1 MF8 > 0.3855 > > > >3 N0620.0120 -18.2750 10.1980 N.pl3 1 MF8 > -0.1861 > > > >4 N0919.1990 -19.7060 11.8570 N.pl3 1 MF8 > -0.1293 > > > >5 C0118.6460 -20.73108.7020 C.3 1 MF8 > 0.0558 > > > >6 N0219.3290 -19.49908.3110 N.pl3 1 MF8 > -0.2675 > > > >7 N0518.6660 -17.35208.6680 N.pl3 1 MF8 > -0.1291 > > > >8 C0419.3130 -18.36709.0550 C.cat 1 MF8 > 0.3896 > > > >9 C0320.0370 -19.61707.0360 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 -21.47997.9546 H 1 MF8 > 0.0619 > > > > 15 H 17.5973 -20.54208.7994 H 1 MF8 > 0.0619 > > > > 16 H 19.0353 -21.07299.6382 H 1 MF8 > 0.0619 > > > > 17 H 18.1443 -17.38947.8339 H 1 MF8 > 0.3062 > > > > 18 H 19.9010 -20.60266.6424 H 1 MF8 > 0.0619 > > > > 19 H 21.0802 -19.43497.1891 H 1 MF8 > 0.0619 > > > > 20 H 19.6476 -18.89976.3441 H 1 MF8 > 0.0619 > > > > @BOND > > > > 1 1 21 > > > > 2 1101 > > > > 3 1111 > > > > 4 2 31 > > > > 5 2 42 > > > > 6 3 81 > > > > 7 3121 > > > > 8 4131 > > > > 9 5 61 > > > > 10 5141 > > > > 11 5151 > > > > 12 5161 > > > > 13 6 91 > > > > 14 6 81 > > > > 15 7 82 > > > > 16 7171 > > > > 17 9181 > > > > 18 9191 > > > > 19 9201 > > > > > > > > > > > > * 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 > > > > * >
Re: [gmx-users] How to reduce the penalty of small molecule from CGenFF
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 @MOLECULE MF8 20 19 0 0 0 SMALL GASTEIGER @ATOM 1 N0819.3800 -17.4900 12.2190 N.pl3 1 MF8 -0.2888 2 C0719.5160 -18.4740 11.4320 C.cat 1 MF8 0.3855 3 N0620.0120 -18.2750 10.1980 N.pl3 1 MF8 -0.1861 4 N0919.1990 -19.7060 11.8570 N.pl3 1 MF8 -0.1293 5 C0118.6460 -20.73108.7020 C.3 1 MF8 0.0558 6 N0219.3290 -19.49908.3110 N.pl3 1 MF8 -0.2675 7 N0518.6660 -17.35208.6680 N.pl3 1 MF8 -0.1291 8 C0419.3130 -18.36709.0550 C.cat 1 MF8 0.3896 9 C0320.0370 -19.61707.0360 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 -21.47997.9546 H 1 MF8 0.0619 15 H 17.5973 -20.54208.7994 H 1 MF8 0.0619 16 H 19.0353 -21.07299.6382 H 1 MF8 0.0619 17 H 18.1443 -17.38947.8339 H 1 MF8 0.3062 18 H 19.9010 -20.60266.6424 H 1 MF8 0.0619 19 H 21.0802 -19.43497.1891 H 1 MF8 0.0619 20 H 19.6476 -18.89976.3441 H 1 MF8 0.0619 @BOND 1 1 21 2 1101 3 1111 4 2 31 5 2 42 6 3 81 7 3121 8 4131 9 5 61 10 5141 11 5151 12 5161 13 6 91 14 6 81 15 7 82 16 7171 17 9181 18 9191 19 9201 * 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 N08NG321 -0.603 !2.500 ATOM C07CG2N1 0.547 !5.000 ATOM N06NG311 -0.430 !6.533 ATOM N09NG2D1 -0.907 !2.500 ATOM C01CG331 -0.141 !9.593 ATOM N02NG301 -0.371 ! 12.315 ATOM N05NG2D1 -0.861 !4.101 ATOM C04CG2N1 0.609 ! 10.954 ATOM C03CG331 -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 HGP10.369 !0.000 ATOM H5 HGA30.090 !2.518 ATOM H6 HGA30.090 !2.518 ATOM H7 HGA30.090 !2.518 ATOM H8 HGP10.369 !0.030 ATOM H9 HGA30.090 !2.518 ATOM H10HGA30.090 !2.518 ATOM H11HGA30.090 !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 C07N09N06N08 IMPR C04N05N02N06 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
