Re: [gmx-users] CHARMM-GUI files give error in Gromacs
Ok I will. Thank you very much Justin. > On 02 Sep 2016, at 16:58, Justin Lemkul wrote: > > > > On 9/2/16 10:44 AM, Justin Lemkul wrote: >> >> >> On 9/2/16 10:43 AM, gozde ergin wrote: >>> Ok I understand. I did exactly same thing for another molecule (SDS) and >>> everything is working without any error. >>> But I do not know what should I do with cis-pinonic. >>> >> >> If you upload a tarball of all the GROMACS files provided by CHARMM-GUI, I >> will >> take a quick look. >> > > Contact the CHARMM-GUI developers. The problem is that the parameters > specific to the cis-pinonic acid present in lig/lig.prm have not been > included when the force field was converted, so only parameters in the ligand > that are taken from the parent force field are present. So their conversion > script has a bug. > > -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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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.
Re: [gmx-users] CHARMM-GUI files give error in Gromacs
On 9/2/16 10:44 AM, Justin Lemkul wrote: On 9/2/16 10:43 AM, gozde ergin wrote: Ok I understand. I did exactly same thing for another molecule (SDS) and everything is working without any error. But I do not know what should I do with cis-pinonic. If you upload a tarball of all the GROMACS files provided by CHARMM-GUI, I will take a quick look. Contact the CHARMM-GUI developers. The problem is that the parameters specific to the cis-pinonic acid present in lig/lig.prm have not been included when the force field was converted, so only parameters in the ligand that are taken from the parent force field are present. So their conversion script has a bug. -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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] CHARMM-GUI files give error in Gromacs
On 9/2/16 10:43 AM, gozde ergin wrote: Ok I understand. I did exactly same thing for another molecule (SDS) and everything is working without any error. But I do not know what should I do with cis-pinonic. If you upload a tarball of all the GROMACS files provided by CHARMM-GUI, I will take a quick look. -Justin On 02 Sep 2016, at 16:40, Justin Lemkul wrote: On 9/2/16 10:39 AM, gozde ergin wrote: Hi Justin, I try to use the CHARMM-GUI files directly. My purpose is simulating the water and ci-pinonic system. Cis-pionic molecules will stay on the water surface and I would like to estimate surface tension reduction. What should I change in CHARMM-GUI files? Nothing. That's my point. When the system is constructed, CHARMM-GUI builds a PSF and list of force field parameters that it needs. This information is then converted to GROMACS format. CHARMM-GUI does an energy evaluation to confirm that everything is present. That's why it's a bit mystifying that GROMACS fails; by definition, the system, topology, and force field have already been checked for integrity. -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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- == 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] CHARMM-GUI files give error in Gromacs
Ok I understand. I did exactly same thing for another molecule (SDS) and everything is working without any error. But I do not know what should I do with cis-pinonic. > On 02 Sep 2016, at 16:40, Justin Lemkul wrote: > > > > On 9/2/16 10:39 AM, gozde ergin wrote: >> Hi Justin, >> >> I try to use the CHARMM-GUI files directly. My purpose is simulating the >> water and ci-pinonic system. Cis-pionic molecules will stay on the water >> surface and I would like to estimate surface tension reduction. >> >> What should I change in CHARMM-GUI files? > > Nothing. That's my point. When the system is constructed, CHARMM-GUI builds > a PSF and list of force field parameters that it needs. This information is > then converted to GROMACS format. CHARMM-GUI does an energy evaluation to > confirm that everything is present. That's why it's a bit mystifying that > GROMACS fails; by definition, the system, topology, and force field have > already been checked for integrity. > > -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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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.
Re: [gmx-users] CHARMM-GUI files give error in Gromacs
On 9/2/16 10:39 AM, gozde ergin wrote: Hi Justin, I try to use the CHARMM-GUI files directly. My purpose is simulating the water and ci-pinonic system. Cis-pionic molecules will stay on the water surface and I would like to estimate surface tension reduction. What should I change in CHARMM-GUI files? Nothing. That's my point. When the system is constructed, CHARMM-GUI builds a PSF and list of force field parameters that it needs. This information is then converted to GROMACS format. CHARMM-GUI does an energy evaluation to confirm that everything is present. That's why it's a bit mystifying that GROMACS fails; by definition, the system, topology, and force field have already been checked for integrity. -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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] CHARMM-GUI files give error in Gromacs
Hi Justin, I try to use the CHARMM-GUI files directly. My purpose is simulating the water and ci-pinonic system. Cis-pionic molecules will stay on the water surface and I would like to estimate surface tension reduction. What should I change in CHARMM-GUI files? > > CHARMM-GUI provides a self-contained force field file that will have > everything you need. It is a subset of the full CHARMM force field plus any > parameters that are newly introduced by your non-standard molecule. Are you > using only files directly from CHARMM-GUI, without modification, or are you > trying to do something else? > > -Justin -- 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] CHARMM-GUI files give error in Gromacs
On 9/2/16 10:28 AM, gozde ergin wrote: Dear all, I used CHARMM-Gui and prepared the .pdb, .itp and .top file for cis pionic acid. After that I used genbox command of gromacs and add some water molecules. When I try to run I get 100 Errors saying : No default bond types, No default U-B types, No default Proper Dih. types, No default Improper Dih. types. All these errors are related to .itp file. However .itp files seems correct: Any help would be appreciated. Thanks. CHARMM-GUI provides a self-contained force field file that will have everything you need. It is a subset of the full CHARMM force field plus any parameters that are newly introduced by your non-standard molecule. Are you using only files directly from CHARMM-GUI, without modification, or are you trying to do something else? -Justin ;; ;; Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.7 ;; ;; psf2itp_mol.py ;; ;; Correspondance: ;; j712l...@ku.edu or won...@ku.edu ;; ;; GROMACS topology file for LIG ;; [ moleculetype ] ; name nrexcl LIG 3 [ atoms ] ; nrtyperesnr residu atomcgnrcharge mass 1 CG3C41 1 LIG C2 1 -0.08712.0110 ; qtot -0.087 2 CG3C41 1 LIG C1 2 -0.04612.0110 ; qtot -0.133 3 HGA1 1 LIG H1 3 0.090 1.0080 ; qtot -0.043 4 CG3C41 1 LIG C3 4 -0.03812.0110 ; qtot -0.081 5 CG2O5 1 LIG C8 5 0.38812.0110 ; qtot 0.307 6 HGA1 1 LIG H2 6 0.090 1.0080 ; qtot 0.397 7 OG2D3 1 LIG O1 7 -0.48115.9994 ; qtot -0.084 8 CG331 1 LIGC10 8 -0.22912.0110 ; qtot -0.313 9 HGA3 1 LIGH14 9 0.090 1.0080 ; qtot -0.223 10 HGA3 1 LIGH15 10 0.090 1.0080 ; qtot -0.133 11 HGA3 1 LIGH13 11 0.090 1.0080 ; qtot -0.043 12 CG3C41 1 LIG C4 12 -0.17812.0110 ; qtot -0.221 13 HGA2 1 LIG H4 13 0.090 1.0080 ; qtot -0.131 14 HGA2 1 LIG H3 14 0.090 1.0080 ; qtot -0.041 15 CG331 1 LIG C6 15 -0.24812.0110 ; qtot -0.289 16 HGA3 1 LIGH10 16 0.090 1.0080 ; qtot -0.199 17 HGA3 1 LIG H9 17 0.090 1.0080 ; qtot -0.109 18 HGA3 1 LIG H8 18 0.090 1.0080 ; qtot -0.019 19 CG331 1 LIG C5 19 -0.24812.0110 ; qtot -0.267 20 HGA3 1 LIG H6 20 0.090 1.0080 ; qtot -0.177 21 HGA3 1 LIG H7 21 0.090 1.0080 ; qtot -0.087 22 HGA3 1 LIG H5 22 0.090 1.0080 ; qtot 0.003 23 CG321 1 LIG C7 23 -0.20712.0110 ; qtot -0.204 24 CG2O2 1 LIG C9 24 0.80312.0110 ; qtot 0.599 25 HGA2 1 LIGH12 25 0.090 1.0080 ; qtot 0.689 26 HGA2 1 LIGH11 26 0.090 1.0080 ; qtot 0.779 27 OG2D1 1 LIG O3 27 -0.57615.9994 ; qtot 0.203 28 OG311 1 LIG O2 28 -0.63215.9994 ; qtot -0.429 29 HGP1 1 LIGH16 29 0.429 1.0080 ; qtot 0.000 [ bonds ] ; aiaj funct b0 Kb 1 2 1 1 3 1 112 1 123 1 2 4 1 215 1 219 1 4 5 1 4 6 1 412 1 5 7 1 5 8 1 8 9 1 810 1 811 1 1213 1 1214 1 1516 1 1517 1 1518 1 1920 1 1921 1 1922 1 2324 1 2325 1 2326 1 2427 1 2428 1 2829 1 [ pairs ] ; aiaj funct c6 c12 1 2 1 1 5 1 1 6 1 112 1 116 1 117 1 118 1 120 1 121 1 122 1 127 1 128 1 2 4 1 2 7 1 2 8 1 213 1 214 1 224 1 225 1 226 1 3 4 1 313 1 314 1 315 1 319 1 324 1 325 1 326 1 4 9 1 410 1 411 1 412 1 416 1 417 1 418 1 420 1 421 1 422 1 423 1 513 1 514
[gmx-users] CHARMM-GUI files give error in Gromacs
Dear all, I used CHARMM-Gui and prepared the .pdb, .itp and .top file for cis pionic acid. After that I used genbox command of gromacs and add some water molecules. When I try to run I get 100 Errors saying : No default bond types, No default U-B types, No default Proper Dih. types, No default Improper Dih. types. All these errors are related to .itp file. However .itp files seems correct: Any help would be appreciated. Thanks. ;; ;; Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.7 ;; ;; psf2itp_mol.py ;; ;; Correspondance: ;; j712l...@ku.edu or won...@ku.edu ;; ;; GROMACS topology file for LIG ;; [ moleculetype ] ; name nrexcl LIG 3 [ atoms ] ; nrtyperesnr residu atomcgnrcharge mass 1 CG3C41 1 LIG C2 1 -0.08712.0110 ; qtot -0.087 2 CG3C41 1 LIG C1 2 -0.04612.0110 ; qtot -0.133 3 HGA1 1 LIG H1 3 0.090 1.0080 ; qtot -0.043 4 CG3C41 1 LIG C3 4 -0.03812.0110 ; qtot -0.081 5 CG2O5 1 LIG C8 5 0.38812.0110 ; qtot 0.307 6 HGA1 1 LIG H2 6 0.090 1.0080 ; qtot 0.397 7 OG2D3 1 LIG O1 7 -0.48115.9994 ; qtot -0.084 8 CG331 1 LIGC10 8 -0.22912.0110 ; qtot -0.313 9 HGA3 1 LIGH14 9 0.090 1.0080 ; qtot -0.223 10 HGA3 1 LIGH15 10 0.090 1.0080 ; qtot -0.133 11 HGA3 1 LIGH13 11 0.090 1.0080 ; qtot -0.043 12 CG3C41 1 LIG C4 12 -0.17812.0110 ; qtot -0.221 13 HGA2 1 LIG H4 13 0.090 1.0080 ; qtot -0.131 14 HGA2 1 LIG H3 14 0.090 1.0080 ; qtot -0.041 15 CG331 1 LIG C6 15 -0.24812.0110 ; qtot -0.289 16 HGA3 1 LIGH10 16 0.090 1.0080 ; qtot -0.199 17 HGA3 1 LIG H9 17 0.090 1.0080 ; qtot -0.109 18 HGA3 1 LIG H8 18 0.090 1.0080 ; qtot -0.019 19 CG331 1 LIG C5 19 -0.24812.0110 ; qtot -0.267 20 HGA3 1 LIG H6 20 0.090 1.0080 ; qtot -0.177 21 HGA3 1 LIG H7 21 0.090 1.0080 ; qtot -0.087 22 HGA3 1 LIG H5 22 0.090 1.0080 ; qtot 0.003 23 CG321 1 LIG C7 23 -0.20712.0110 ; qtot -0.204 24 CG2O2 1 LIG C9 24 0.80312.0110 ; qtot 0.599 25 HGA2 1 LIGH12 25 0.090 1.0080 ; qtot 0.689 26 HGA2 1 LIGH11 26 0.090 1.0080 ; qtot 0.779 27 OG2D1 1 LIG O3 27 -0.57615.9994 ; qtot 0.203 28 OG311 1 LIG O2 28 -0.63215.9994 ; qtot -0.429 29 HGP1 1 LIGH16 29 0.429 1.0080 ; qtot 0.000 [ bonds ] ; aiaj funct b0 Kb 1 2 1 1 3 1 112 1 123 1 2 4 1 215 1 219 1 4 5 1 4 6 1 412 1 5 7 1 5 8 1 8 9 1 810 1 811 1 1213 1 1214 1 1516 1 1517 1 1518 1 1920 1 1921 1 1922 1 2324 1 2325 1 2326 1 2427 1 2428 1 2829 1 [ pairs ] ; aiaj funct c6 c12 1 2 1 1 5 1 1 6 1 112 1 116 1 117 1 118 1 120 1 121 1 122 1 127 1 128 1 2 4 1 2 7 1 2 8 1 213 1 214 1 224 1 225 1 226 1 3 4 1 313 1 314 1 315 1 319 1 324 1 325 1 326 1 4 9 1 410 1 411 1 412 1 416 1 417 1 418 1 420 1 421 1 422 1 423 1 513 1 514 1 515 1 519 1 6 7 1 6 8 1 613 1 614 1 615 1 619 1 7 9 1 710 1 711 1 712 1 812 1 1215 1 1219 1 1224 1 1225 1 1226 1
