Re: [gmx-users] Overriding atom type.
On 12/4/19 1:18 PM, Yogesh Sharma wrote: greetings Dr. Justin I used charmm gui Input generator for ligands. these are H2O2, NO and Urea. I got three files for each Charmm36.itp, ligand.itp and topol. top. I added charmm36.itp files for each ligand under subsequent section with my system.itp and added #include link for ligand.itp files in my topol file. Everything is working fine if, I am simulating them one by one but when combined, system is showing overriding atom type error for common named residues. CHARMM-GUI provides a force field file that contains only the parameters you need for the system you have supplied it. In that way, it differs from a normal force field that already has everything, even parameters you may not need. Given this assumption that CHARMM-GUI makes, editing topologies it provides can be difficult. Any redundant parameters have to be removed if you're going to make changes to the set of files it provides. Or use the CHARMM36 port (which has the full force field) and augment it with any new parameters that the CGenFF program (within CHARMM-GUI) came up with. -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] Overriding atom type.
greetings Dr. Justin I used charmm gui Input generator for ligands. these are H2O2, NO and Urea. I got three files for each Charmm36.itp, ligand.itp and topol. top. I added charmm36.itp files for each ligand under subsequent section with my system.itp and added #include link for ligand.itp files in my topol file. Everything is working fine if, I am simulating them one by one but when combined, system is showing overriding atom type error for common named residues. -- 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] Overriding atom type.
On 12/4/19 6:32 AM, Yogesh Sharma wrote: Thank you Dr. Alessandra I actually generated topologies for my ligands using charmm server generated itp files had few overriding names, which are throwing errors when combined. You can't introduce duplicate parameters. If you have multiple ligands that make use of the same paramters, the directive [atomtypes], [bondtypes], etc. must be merged into a single .itp file and #included. I will note that these atom types are already standard in our CHARMM36 port (including CGenFF) for GROMACS. I don't know which server you used but these should not be new atom types. -Justin Please have a look at the itp files pasted here. ... [ atomtypes ] ; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14 CG2O6 612.0110 0.600 A3.56359487256e-01 2.928800e-01 HGP1 1 1.0080 0.340 A4.00013524445e-02 1.924640e-01 NG2S2 714.0070 -0.690 A3.29632525712e-01 8.368000e-01 OG2D1 815.9994 -0.580 A3.02905564168e-01 5.020800e-01 ; 2.49451641079e-015.020800e-01 [ bondtypes ] ; i j func b0 Kb CG2O6 NG2S2 1 1.36e-01 3.598240e+05 CG2O6 OG2D1 1 1.23e-01 5.439200e+05 NG2S2HGP1 1 1.00e-01 4.016640e+05 [ pairtypes ] ; i j func sigma1-4 epsilon1-4 CG2O6 OG2D1 1 3.02905564168e-01 3.83469934154e-01 HGP1 OG2D1 1 1.44726496762e-01 3.10857403193e-01 NG2S2 OG2D1 1 2.89542083396e-01 6.48182492821e-01 OG2D1 OG2D1 1 2.49451641079e-01 5.0208000e-01 [ angletypes ] ; i j k func th0 cth S0 Kub CG2O6 NG2S2HGP1 5 1.200e+02 4.184e+02 0.000e+00 0.000e+00 HGP1 NG2S2HGP1 5 1.200e+02 1.9246400e+02 0.000e+00 0.000e+00 NG2S2 CG2O6 NG2S2 5 1.150e+02 5.8576000e+02 0.000e+00 0.000e+00 NG2S2 CG2O6 OG2D1 5 1.225e+02 6.276e+02 2.370e-01 4.184e+04 [ dihedraltypes ] ; i j k l func phi0 cp mult NG2S2 CG2O6 NG2S2HGP1 9 1.80e+02 6.276000e+00 2 OG2D1 CG2O6 NG2S2HGP1 9 1.80e+02 5.857600e+00 2 [ dihedraltypes ] ; i j k l func q0 cq CG2O6 NG2S2 NG2S2 OG2D1 2 0.00e+00 6.694400e+02 [ atomtypes ] ; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14 HGP1 1 1.0080 0.369 A4.00013524445e-02 1.924640e-01 NG2D1 714.0070 -0.370 A3.29632525712e-01 8.368000e-01 OG2D1 815.9994 0.001 A3.02905564168e-01 5.020800e-01 ; 2.49451641079e-015.020800e-01 [ bondtypes ] ; i j func b0 Kb NG2D1HGP1 1 1.00e-01 3.807440e+05 NG2D1 OG2D1 1 1.225000e-01 4.853440e+05 [ pairtypes ] ; i j func sigma1-4 epsilon1-4 HGP1 OG2D1 1 1.44726496762e-01 3.10857403193e-01 NG2D1 OG2D1 1 2.89542083396e-01 6.48182492821e-01 OG2D1 OG2D1 1 2.49451641079e-01 5.0208000e-01 [ angletypes ] ; i j k func th0 cth S0 Kub OG2D1 NG2D1HGP1 5 1.130e+02 4.1003200e+02 0.000e+00 0.000e+00 [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.0 1.0 [ atomtypes ] ; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14 HGP1 1 1.0080 0.500 A4.00013524445e-02 1.924640e-01 OG311 815.9994 -0.500 A3.14487247504e-01 8.037464e-01 [ bondtypes ] ; i j func b0 Kb OG311HGP1 1 9.60e-02 4.560560e+05 OG311 OG311 1 1.42e-01 3.581504e+05 [ angletypes ] ; i j k func th0 cth S0 Kub OG311 OG311HGP1 5 1.015e+02 5.0208000e+02 0.000e+00 0.000e+00 [ dihedraltypes ] ; i j k l func phi0 cp mult HGP1 OG311 OG311HGP1 9 0.00e+00 7.531200e-01 3 .. I just combined files into my system itp file (solvated membrane protein) Can i simulate these three molecules together? -- == 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!
Re: [gmx-users] Overriding atom type.
Thank you Dr. Alessandra I actually generated topologies for my ligands using charmm server generated itp files had few overriding names, which are throwing errors when combined. Please have a look at the itp files pasted here. ... [ atomtypes ] ; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14 CG2O6 612.0110 0.600 A3.56359487256e-01 2.928800e-01 HGP1 1 1.0080 0.340 A4.00013524445e-02 1.924640e-01 NG2S2 714.0070 -0.690 A3.29632525712e-01 8.368000e-01 OG2D1 815.9994 -0.580 A3.02905564168e-01 5.020800e-01 ; 2.49451641079e-015.020800e-01 [ bondtypes ] ; i j func b0 Kb CG2O6 NG2S2 1 1.36e-01 3.598240e+05 CG2O6 OG2D1 1 1.23e-01 5.439200e+05 NG2S2HGP1 1 1.00e-01 4.016640e+05 [ pairtypes ] ; i j func sigma1-4 epsilon1-4 CG2O6 OG2D1 1 3.02905564168e-01 3.83469934154e-01 HGP1 OG2D1 1 1.44726496762e-01 3.10857403193e-01 NG2S2 OG2D1 1 2.89542083396e-01 6.48182492821e-01 OG2D1 OG2D1 1 2.49451641079e-01 5.0208000e-01 [ angletypes ] ; i j k func th0 cth S0 Kub CG2O6 NG2S2HGP1 5 1.200e+02 4.184e+02 0.000e+00 0.000e+00 HGP1 NG2S2HGP1 5 1.200e+02 1.9246400e+02 0.000e+00 0.000e+00 NG2S2 CG2O6 NG2S2 5 1.150e+02 5.8576000e+02 0.000e+00 0.000e+00 NG2S2 CG2O6 OG2D1 5 1.225e+02 6.276e+02 2.370e-01 4.184e+04 [ dihedraltypes ] ; i j k l func phi0 cp mult NG2S2 CG2O6 NG2S2HGP1 9 1.80e+02 6.276000e+00 2 OG2D1 CG2O6 NG2S2HGP1 9 1.80e+02 5.857600e+00 2 [ dihedraltypes ] ; i j k l func q0 cq CG2O6 NG2S2 NG2S2 OG2D1 2 0.00e+00 6.694400e+02 [ atomtypes ] ; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14 HGP1 1 1.0080 0.369 A4.00013524445e-02 1.924640e-01 NG2D1 714.0070 -0.370 A3.29632525712e-01 8.368000e-01 OG2D1 815.9994 0.001 A3.02905564168e-01 5.020800e-01 ; 2.49451641079e-015.020800e-01 [ bondtypes ] ; i j func b0 Kb NG2D1HGP1 1 1.00e-01 3.807440e+05 NG2D1 OG2D1 1 1.225000e-01 4.853440e+05 [ pairtypes ] ; i j func sigma1-4 epsilon1-4 HGP1 OG2D1 1 1.44726496762e-01 3.10857403193e-01 NG2D1 OG2D1 1 2.89542083396e-01 6.48182492821e-01 OG2D1 OG2D1 1 2.49451641079e-01 5.0208000e-01 [ angletypes ] ; i j k func th0 cth S0 Kub OG2D1 NG2D1HGP1 5 1.130e+02 4.1003200e+02 0.000e+00 0.000e+00 [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.0 1.0 [ atomtypes ] ; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14 HGP1 1 1.0080 0.500 A4.00013524445e-02 1.924640e-01 OG311 815.9994 -0.500 A3.14487247504e-01 8.037464e-01 [ bondtypes ] ; i j func b0 Kb OG311HGP1 1 9.60e-02 4.560560e+05 OG311 OG311 1 1.42e-01 3.581504e+05 [ angletypes ] ; i j k func th0 cth S0 Kub OG311 OG311HGP1 5 1.015e+02 5.0208000e+02 0.000e+00 0.000e+00 [ dihedraltypes ] ; i j k l func phi0 cp mult HGP1 OG311 OG311HGP1 9 0.00e+00 7.531200e-01 3 .. I just combined files into my system itp file (solvated membrane protein) Can i simulate these three molecules together? -- 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] Overriding atom type.
Hi, On Wed, Dec 4, 2019 at 7:41 AM Yogesh Sharma wrote: > Hello Users, > I was trying to run grompp for a membrane protein - ligand dynamics. I am > using 4 5 ligands together. Under grompp run I got error overriding > atomtype HGP1. Came out two ligands were sharing similar naming in atomtype > section. I wanted to ask is it harmless to change it manually are there any > conventions for it ? following this are there any other changes in > topology file that i need to make? > [ atomtypes ] > ; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14 >CG2O6 612.0110 0.600 A3.56359487256e-01 > 2.928800e-01 > HGP1 1 1.0080 0.340 A4.00013524445e-02 > 1.924640e-01 >NG2S2 714.0070 -0.690 A3.29632525712e-01 > 8.368000e-01 >OG2D1 815.9994 -0.580 A3.02905564168e-01 > 5.020800e-01 ; > [ atomtypes ] > ; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14 > HGP1 1 1.0080 0.500 A4.00013524445e-02 > 1.924640e-01 >OG311 815.9994 -0.500 A3.14487247504e-01 > 8.037464e-01 > [ atomtypes ] section in the top file is used to to customize your non-bonded parameters One can use this section to define new atom types, but this should take place in line with the rest of the force field parameters. In the above case I have noticed that non-bonded parameters (LJ) for HGP1 are identical in the two [ atomtypes ], and the atomic charge values are readed from the top file section [atoms]. If it is the case, you do not need to define it twice. Best regards Alessandra Do you used custermized non-bonded parameters ? > * thank you for your precious time.* > > * with regards* > *Yogesh Sharma* > -- > 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. > -- 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.
[gmx-users] Overriding atom type.
Hello Users, I was trying to run grompp for a membrane protein - ligand dynamics. I am using 4 5 ligands together. Under grompp run I got error overriding atomtype HGP1. Came out two ligands were sharing similar naming in atomtype section. I wanted to ask is it harmless to change it manually are there any conventions for it ? following this are there any other changes in topology file that i need to make? [ atomtypes ] ; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14 CG2O6 612.0110 0.600 A3.56359487256e-01 2.928800e-01 HGP1 1 1.0080 0.340 A4.00013524445e-02 1.924640e-01 NG2S2 714.0070 -0.690 A3.29632525712e-01 8.368000e-01 OG2D1 815.9994 -0.580 A3.02905564168e-01 5.020800e-01 ; [ atomtypes ] ; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14 HGP1 1 1.0080 0.500 A4.00013524445e-02 1.924640e-01 OG311 815.9994 -0.500 A3.14487247504e-01 8.037464e-01 * thank you for your precious time.* * with regards* *Yogesh Sharma* -- 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.
