Re: [gmx-users] pdb2gmx error due to terminal capping of peptide
Hi, Leave the rtp the way it was and name the residue in the pdb file so that it matches. Then you won't have to teach pdb2gmx that your newly invented residue is protein Mark On Fri., 25 Jan. 2019, 05:51 Neena Susan Eappen, < neena.susaneap...@mail.utoronto.ca> wrote: > Hi GMX users, > > > 1. I drew the structure of my target peptide on Pymol, added amide > capping group (NHH) at C terminus of peptide > 2. Typed in the command: gmx pdb2gmx –f A15K.pdb –o A15K.gro –ter –ignh > 3. Chose AMBER99sb-ildn force field which has parameters for NH2 > capping group > 4. Fatal error > 5. Changed naming of amide group in .rtp file of AMBER99sb-ildn from > NH2 to NHH so that naming is similar to .pdb file. > 6. Still fatal error. > The residues in the chain ALA16--NHH32 do not have a consistent type. The > first residue has type 'Protein', while residue NHH32 is of type 'Other'. > Either there is a mistake in your chain, or it includes nonstandard residue > names that have not yet been added to the residuetypes.dat file in the > GROMACS library directory. > > Any insight would be appreciated, > Thank you, > Neena > -- > 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] pdb2gmx error due to terminal capping of peptide
Hi GMX users, 1. I drew the structure of my target peptide on Pymol, added amide capping group (NHH) at C terminus of peptide 2. Typed in the command: gmx pdb2gmx –f A15K.pdb –o A15K.gro –ter –ignh 3. Chose AMBER99sb-ildn force field which has parameters for NH2 capping group 4. Fatal error 5. Changed naming of amide group in .rtp file of AMBER99sb-ildn from NH2 to NHH so that naming is similar to .pdb file. 6. Still fatal error. The residues in the chain ALA16--NHH32 do not have a consistent type. The first residue has type 'Protein', while residue NHH32 is of type 'Other'. Either there is a mistake in your chain, or it includes nonstandard residue names that have not yet been added to the residuetypes.dat file in the GROMACS library directory. Any insight would be appreciated, Thank you, Neena -- 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] pdb2gmx error
Hi, Why is your residue numbering and residue naming changing in mutually inconsistent ways? Mark On Thu, Jun 16, 2016 at 9:36 AM bharat gupta wrote: > Hi, > > I have been trying to build the toplogy for cellopentoase using the newly > derived parameters mentioned in this paper: > http://www.ncbi.nlm.nih.gov/pubmed/21387332. I got the paper from the > gromacs website: > http://www.gromacs.org/@api/deki/files/200/=56a_CARBO4GROMACS.rar > > When I try to construct the topology file using this forcefield, I am > getting the following error: > > Fatal error: > Residue 6 named GLCN of a molecule in the input file was mapped > to an entry in the topology database, but the atom C1 used in > that entry is not found in the input file. Perhaps your atom > and/or residue naming needs to be fixed. > > I have only 5 residues in the pdb file, but gromacs is counting it as 6 > residues. Here's the pdb file: > > HEADER CP5 > ATOM 1 O2 GLC01 7.400 0.776 35.278 0.70 24.55 > O > ATOM 2 C2 GLC01 6.024 0.721 35.632 0.70 23.65 > C > ATOM 3 C3 GLC01 5.240 0.984 34.354 0.70 21.57 > C > ATOM 4 O3 GLC01 5.144 -0.245 33.608 0.70 14.59 > O > ATOM 5 C4 GLC01 3.902 1.571 34.776 0.70 20.91 > C > ATOM 6 O4 GLC01 3.006 1.662 33.670 0.70 19.67 > O > ATOM 7 C5 GLC01 4.174 2.944 35.391 0.70 22.32 > C > ATOM 8 C6 GLC01 2.914 3.605 35.899 0.70 21.51 > C > ATOM 9 O6 GLC01 2.201 2.690 36.737 0.70 20.09 > O > ATOM 10 O5 GLC01 5.080 2.890 36.510 0.70 24.12 > O > ATOM 11 C1 GLC01 5.742 1.651 36.843 0.70 26.75 > C > ATOM 12 O1 GLC 1 5.207 0.892 37.971 0.70 30.32 > O > ATOM 13 C4 GLC 2 4.222 1.340 38.917 0.70 32.87 > C > ATOM 14 C5 GLC 2 4.753 1.239 40.352 0.70 33.51 > C > ATOM 15 O5 GLC 2 3.711 1.506 41.306 0.70 35.29 > O > ATOM 16 C6 GLC 2 5.888 2.194 40.665 0.70 34.02 > C > ATOM 17 O6 GLC 2 5.803 2.537 42.057 0.70 32.97 > O > ATOM 18 C3 GLC 2 3.072 0.331 38.851 0.70 33.72 > C > ATOM 19 O3 GLC 2 2.435 0.360 37.564 0.70 34.01 > O > ATOM 20 C2 GLC 2 2.027 0.450 39.972 0.70 35.29 > C > ATOM 21 O2 GLC 2 1.149 -0.684 39.932 0.70 36.32 > O > ATOM 22 C1 GLC 2 2.684 0.512 41.351 0.70 36.04 > C > ATOM 23 O1 GLC 2 1.704 0.843 42.349 0.70 36.96 > O > ATOM 24 C4 GLC 3 2.032 0.454 43.689 0.70 38.12 > C > ATOM 25 C5 GLC 3 0.810 -0.195 44.344 0.70 38.87 > C > ATOM 26 O5 GLC 3 1.085 -0.507 45.715 0.70 39.40 > O > ATOM 27 C6 GLC 3 0.372 -1.455 43.605 0.70 38.87 > C > ATOM 28 O6 GLC 3 -0.996 -1.300 43.220 0.70 39.09 > O > ATOM 29 C3 GLC 3 2.455 1.683 44.498 0.70 38.55 > C > ATOM 30 O3 GLC 3 3.729 2.152 44.043 0.70 38.93 > O > ATOM 31 C2 GLC 3 2.550 1.405 45.997 0.70 39.25 > C > ATOM 32 O2 GLC 3 2.700 2.646 46.700 0.70 38.44 > O > ATOM 33 C1 GLC 3 1.319 0.663 46.514 0.70 39.97 > C > ATOM 34 O1 GLC 3 1.522 0.333 47.897 0.70 41.30 > O > ATOM 35 C4 GLC 4 0.320 -0.039 48.583 0.70 42.19 > C > ATOM 36 C5 GLC 4 -0.067 0.972 49.664 0.70 42.80 > C > ATOM 37 O5 GLC 4 -1.358 0.617 50.163 0.70 43.08 > O > ATOM 38 C6 GLC 4 -0.082 2.420 49.189 0.70 43.23 > C > ATOM 39 O6 GLC 4 -0.900 2.532 48.019 0.70 43.36 > O > ATOM 40 C3 GLC 4 0.485 -1.387 49.281 0.70 42.24 > C > ATOM 41 O3 GLC 4 0.818 -2.397 48.323 0.70 41.16 > O > ATOM 42 C2 GLC 4 -0.782 -1.783 50.046 0.70 42.64 > C > ATOM 43 O2 GLC 4 -0.470 -2.862 50.935 0.70 42.32 > O > ATOM 44 C1 GLC 4 -1.375 -0.633 50.870 0.70 43.60 > C > ATOM 45 O1 GLCN4 -2.732 -0.947 51.190 0.70 45.14 > O > ATOM 46 C4 GLCN5 -3.137 -0.484 52.482 0.70 46.29 > C > ATOM 47 C3 GLCN5 -4.035 0.750 52.337 0.70 46.70 > C > ATOM 48 O3 GLCN5 -3.269 1.864 51.865 0.70 46.85 > O > ATOM 49 C2 GLCN5 -4.706 1.124 53.659 0.70 47.10 > C > ATOM 50 O2 GLCN5 -5.680 2.147 53.435 0.70 47.17 > O > ATOM 51 C1 GLCN5 -5.377 -0.097 54.282 0.70 47.34 > C > ATOM 52 O1 GLCN5 -5.958 0.264 55.539 0.70 47.48 > O > ATOM 53 O5 GLCN5 -4.397 -1.126 54.467 0.70 47.17 > O > ATOM 54 C5 GLCN5 -3.867 -1.611 53.225 0.70 46.80 > C > ATOM 55 C6 GLCN
Re: [gmx-users] pdb2gmx error
Hi, I have been trying to build the toplogy for cellopentoase using the newly derived parameters mentioned in this paper: http://www.ncbi.nlm.nih.gov/pubmed/21387332. I got the paper from the gromacs website: http://www.gromacs.org/@api/deki/files/200/=56a_CARBO4GROMACS.rar When I try to construct the topology file using this forcefield, I am getting the following error: Fatal error: Residue 6 named GLCN of a molecule in the input file was mapped to an entry in the topology database, but the atom C1 used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. I have only 5 residues in the pdb file, but gromacs is counting it as 6 residues. Here's the pdb file: HEADER CP5 ATOM 1 O2 GLC01 7.400 0.776 35.278 0.70 24.55 O ATOM 2 C2 GLC01 6.024 0.721 35.632 0.70 23.65 C ATOM 3 C3 GLC01 5.240 0.984 34.354 0.70 21.57 C ATOM 4 O3 GLC01 5.144 -0.245 33.608 0.70 14.59 O ATOM 5 C4 GLC01 3.902 1.571 34.776 0.70 20.91 C ATOM 6 O4 GLC01 3.006 1.662 33.670 0.70 19.67 O ATOM 7 C5 GLC01 4.174 2.944 35.391 0.70 22.32 C ATOM 8 C6 GLC01 2.914 3.605 35.899 0.70 21.51 C ATOM 9 O6 GLC01 2.201 2.690 36.737 0.70 20.09 O ATOM 10 O5 GLC01 5.080 2.890 36.510 0.70 24.12 O ATOM 11 C1 GLC01 5.742 1.651 36.843 0.70 26.75 C ATOM 12 O1 GLC 1 5.207 0.892 37.971 0.70 30.32 O ATOM 13 C4 GLC 2 4.222 1.340 38.917 0.70 32.87 C ATOM 14 C5 GLC 2 4.753 1.239 40.352 0.70 33.51 C ATOM 15 O5 GLC 2 3.711 1.506 41.306 0.70 35.29 O ATOM 16 C6 GLC 2 5.888 2.194 40.665 0.70 34.02 C ATOM 17 O6 GLC 2 5.803 2.537 42.057 0.70 32.97 O ATOM 18 C3 GLC 2 3.072 0.331 38.851 0.70 33.72 C ATOM 19 O3 GLC 2 2.435 0.360 37.564 0.70 34.01 O ATOM 20 C2 GLC 2 2.027 0.450 39.972 0.70 35.29 C ATOM 21 O2 GLC 2 1.149 -0.684 39.932 0.70 36.32 O ATOM 22 C1 GLC 2 2.684 0.512 41.351 0.70 36.04 C ATOM 23 O1 GLC 2 1.704 0.843 42.349 0.70 36.96 O ATOM 24 C4 GLC 3 2.032 0.454 43.689 0.70 38.12 C ATOM 25 C5 GLC 3 0.810 -0.195 44.344 0.70 38.87 C ATOM 26 O5 GLC 3 1.085 -0.507 45.715 0.70 39.40 O ATOM 27 C6 GLC 3 0.372 -1.455 43.605 0.70 38.87 C ATOM 28 O6 GLC 3 -0.996 -1.300 43.220 0.70 39.09 O ATOM 29 C3 GLC 3 2.455 1.683 44.498 0.70 38.55 C ATOM 30 O3 GLC 3 3.729 2.152 44.043 0.70 38.93 O ATOM 31 C2 GLC 3 2.550 1.405 45.997 0.70 39.25 C ATOM 32 O2 GLC 3 2.700 2.646 46.700 0.70 38.44 O ATOM 33 C1 GLC 3 1.319 0.663 46.514 0.70 39.97 C ATOM 34 O1 GLC 3 1.522 0.333 47.897 0.70 41.30 O ATOM 35 C4 GLC 4 0.320 -0.039 48.583 0.70 42.19 C ATOM 36 C5 GLC 4 -0.067 0.972 49.664 0.70 42.80 C ATOM 37 O5 GLC 4 -1.358 0.617 50.163 0.70 43.08 O ATOM 38 C6 GLC 4 -0.082 2.420 49.189 0.70 43.23 C ATOM 39 O6 GLC 4 -0.900 2.532 48.019 0.70 43.36 O ATOM 40 C3 GLC 4 0.485 -1.387 49.281 0.70 42.24 C ATOM 41 O3 GLC 4 0.818 -2.397 48.323 0.70 41.16 O ATOM 42 C2 GLC 4 -0.782 -1.783 50.046 0.70 42.64 C ATOM 43 O2 GLC 4 -0.470 -2.862 50.935 0.70 42.32 O ATOM 44 C1 GLC 4 -1.375 -0.633 50.870 0.70 43.60 C ATOM 45 O1 GLCN4 -2.732 -0.947 51.190 0.70 45.14 O ATOM 46 C4 GLCN5 -3.137 -0.484 52.482 0.70 46.29 C ATOM 47 C3 GLCN5 -4.035 0.750 52.337 0.70 46.70 C ATOM 48 O3 GLCN5 -3.269 1.864 51.865 0.70 46.85 O ATOM 49 C2 GLCN5 -4.706 1.124 53.659 0.70 47.10 C ATOM 50 O2 GLCN5 -5.680 2.147 53.435 0.70 47.17 O ATOM 51 C1 GLCN5 -5.377 -0.097 54.282 0.70 47.34 C ATOM 52 O1 GLCN5 -5.958 0.264 55.539 0.70 47.48 O ATOM 53 O5 GLCN5 -4.397 -1.126 54.467 0.70 47.17 O ATOM 54 C5 GLCN5 -3.867 -1.611 53.225 0.70 46.80 C ATOM 55 C6 GLCN5 -2.967 -2.814 53.497 0.70 46.93 C ATOM 56 O6 GLCN5 -1.934 -2.454 54.421 0.70 47.39 O END Can anyone let me know what am I doing wrong? I am trying to perform MD simulation of protein with cellopentoase. So, in order to obtain the parameters for cellopentoase, I am following the parameters mentioned above. -- *Best Regards* Bharat -- Gromacs Users mailing list * Ple
Re: [gmx-users] pdb2gmx error after switching force fields
On 5/13/16 11:04 AM, Irem Altan wrote: Hi, Thanks for the quick reply. Erasing the dihedral with CB worked. I’m actually using Gromacs 5.1.2. Not sure how that's possible. It should have been fixed prior to the release of 5.1.1. -Justin Best, Irem On May 13, 2016, at 10:52 AM, Justin Lemkul wrote: On 5/13/16 10:49 AM, Irem Altan wrote: Hi, I have a .pdb file that I’ve used in simulations with amber99sb before. I have recently switched to amber03. When I do pdb2gmx, I get the following warning: WARNING: WARNING: Residue 26 named GLY of a molecule in the input file was mapped to an entry in the topology database, but the atom CB used in an interaction of type dihedral in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. There is an error in the AMBER03 .rtp file. Either delete the dihedral that calls for CB or upgrade your GROMACS version. I fixed this nearly two years ago, so you're using something really outdated :) The same thing is repeated for a number of residues (26, 51, 59, 66, 67, 83, 85, 95). The weird thing is, the residue numbers in the pdb file start from 107, and gmx complains about lower numbers. Also, have I understood correctly that gmx complains that glycines in my input file don’t have beta carbons? What could be the problem here? pdb2gmx uses its own internal numbering, starting from 1. -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] pdb2gmx error after switching force fields
Hi, Thanks for the quick reply. Erasing the dihedral with CB worked. I’m actually using Gromacs 5.1.2. Best, Irem > On May 13, 2016, at 10:52 AM, Justin Lemkul wrote: > > > > On 5/13/16 10:49 AM, Irem Altan wrote: >> Hi, >> >> I have a .pdb file that I’ve used in simulations with amber99sb before. I >> have recently switched to amber03. When I do pdb2gmx, I get the following >> warning: >> >> WARNING: WARNING: Residue 26 named GLY of a molecule in the input file was >> mapped >> to an entry in the topology database, but the atom CB used in >> an interaction of type dihedral in that entry is not found in the >> input file. Perhaps your atom and/or residue naming needs to be >> fixed. >> > > There is an error in the AMBER03 .rtp file. Either delete the dihedral that > calls for CB or upgrade your GROMACS version. I fixed this nearly two years > ago, so you're using something really outdated :) > >> The same thing is repeated for a number of residues (26, 51, 59, 66, 67, 83, >> 85, 95). The weird thing is, the residue numbers in the pdb file start from >> 107, and gmx complains about lower numbers. Also, have I understood >> correctly that gmx complains that glycines in my input file don’t have beta >> carbons? What could be the problem here? >> > > pdb2gmx uses its own internal numbering, starting from 1. > > -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] pdb2gmx error after switching force fields
On 5/13/16 10:49 AM, Irem Altan wrote: Hi, I have a .pdb file that I’ve used in simulations with amber99sb before. I have recently switched to amber03. When I do pdb2gmx, I get the following warning: WARNING: WARNING: Residue 26 named GLY of a molecule in the input file was mapped to an entry in the topology database, but the atom CB used in an interaction of type dihedral in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. There is an error in the AMBER03 .rtp file. Either delete the dihedral that calls for CB or upgrade your GROMACS version. I fixed this nearly two years ago, so you're using something really outdated :) The same thing is repeated for a number of residues (26, 51, 59, 66, 67, 83, 85, 95). The weird thing is, the residue numbers in the pdb file start from 107, and gmx complains about lower numbers. Also, have I understood correctly that gmx complains that glycines in my input file don’t have beta carbons? What could be the problem here? pdb2gmx uses its own internal numbering, starting from 1. -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.
[gmx-users] pdb2gmx error after switching force fields
Hi, I have a .pdb file that I’ve used in simulations with amber99sb before. I have recently switched to amber03. When I do pdb2gmx, I get the following warning: WARNING: WARNING: Residue 26 named GLY of a molecule in the input file was mapped to an entry in the topology database, but the atom CB used in an interaction of type dihedral in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. The same thing is repeated for a number of residues (26, 51, 59, 66, 67, 83, 85, 95). The weird thing is, the residue numbers in the pdb file start from 107, and gmx complains about lower numbers. Also, have I understood correctly that gmx complains that glycines in my input file don’t have beta carbons? What could be the problem here? Best, Irem -- 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] pdb2gmx error
Indeed Justin I have tried to add the entries for the capped groups in the Amber99SB-ILDN force field (like in the charmm*.ff) since they are not present in aminoacids.n.tdb and aminoacids.c.tdb, so I think I have broken something Stéphane On 4/5/16 6:47 AM, ABEL Stephane 175950 wrote: > Hello, > > When i use pdb2gmx (v.504) and 12 AA long peptide with the Amber99SB-ILDN > force field, I have the error : > Fatal error: > tpA = 53191, i= 0 in print_atoms > > I have no idea what does this message mean. Could you help me? > This shouldn't happen. Have you or anyone else modified the code or force field files? That's the only instance in which this would be triggered. -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] pdb2gmx error
On 4/5/16 6:47 AM, ABEL Stephane 175950 wrote: Hello, When i use pdb2gmx (v.504) and 12 AA long peptide with the Amber99SB-ILDN force field, I have the error : Fatal error: tpA = 53191, i= 0 in print_atoms I have no idea what does this message mean. Could you help me? This shouldn't happen. Have you or anyone else modified the code or force field files? That's the only instance in which this would be triggered. -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.
[gmx-users] pdb2gmx error
Hello, When i use pdb2gmx (v.504) and 12 AA long peptide with the Amber99SB-ILDN force field, I have the error : Fatal error: tpA = 53191, i= 0 in print_atoms I have no idea what does this message mean. Could you help me? Thanks -- 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] pdb2gmx error
On 10/15/15 4:18 AM, Dries Van Rompaey wrote: I did some more testing, it seems that this only occurs when the PRO residue is preceded by a glycine. Could this be related to this issue: http://comments.gmane.org/gmane.science.biology.gromacs.user/72687 ? When I change the glycine residue to anything else, pdb2gmx works like a charm. I constructed a simple test system in which I can replicate the error (see below). Indeed, it seems that the AMBER03 version of GLY has a bunch of dihedrals defined that shouldn't be. It also looks like it is the only AMBER force field that does this, so it's clearly a mistake. I will submit a patch for the 5.1 series. Thanks for digging into this. -Justin REMARK 99 MOE v2014.09 (Chemical Computing Group Inc.) Thu Oct 15 10:05:39 2015 ATOM 1 N ALA 1 0.268 -1.146 -1.547 1.00 0.00 N1+ ATOM 2 CA ALA 1 0.506 0.327 -1.714 1.00 0.00 C ATOM 3 CB ALA 1 -0.837 1.004 -1.931 1.00 0.00 C ATOM 4 C ALA 1 1.226 0.877 -0.480 1.00 0.00 C ATOM 5 O ALA 1 1.399 0.165 0.509 1.00 0.00 O ATOM 6 H1 ALA 1 -0.272 -1.324 -0.688 1.00 0.00 H ATOM 7 H2 ALA 1 -0.224 -1.571 -2.343 1.00 0.00 H ATOM 8 H3 ALA 1 1.161 -1.641 -1.413 1.00 0.00 H ATOM 9 HA ALA 1 1.151 0.435 -2.592 1.00 0.00 H ATOM 10 HB1 ALA 1 -1.364 0.570 -2.788 1.00 0.00 H ATOM 11 HB2 ALA 1 -1.480 0.906 -1.049 1.00 0.00 H ATOM 12 HB3 ALA 1 -0.710 2.074 -2.125 1.00 0.00 H ATOM 13 N GLY 2 1.667 2.171 -0.583 1.00 0.00 N ATOM 14 CA GLY 2 2.390 2.835 0.493 1.00 0.00 C ATOM 15 C GLY 2 2.792 4.221 0.005 1.00 0.00 C ATOM 16 O GLY 2 2.258 4.706 -0.997 1.00 0.00 O ATOM 17 H GLY 2 1.519 2.744 -1.415 1.00 0.00 H ATOM 18 HA1 GLY 2 1.730 2.918 1.361 1.00 0.00 H ATOM 19 HA2 GLY 2 3.269 2.234 0.743 1.00 0.00 H ATOM 20 N PRO 3 3.764 4.872 0.730 1.00 0.00 N ATOM 21 CD PRO 3 4.331 4.472 2.006 1.00 0.00 C ATOM 22 CG PRO 3 4.793 5.786 2.610 1.00 0.00 C ATOM 23 CB PRO 3 5.270 6.581 1.399 1.00 0.00 C ATOM 24 CA PRO 3 4.347 6.129 0.260 1.00 0.00 C ATOM 25 C PRO 3 5.168 5.908 -1.021 1.00 0.00 C ATOM 26 O PRO 3 5.520 4.796 -1.412 1.00 0.00 O ATOM 27 HA PRO 3 3.538 6.843 0.069 1.00 0.00 H ATOM 28 HB1 PRO 3 6.318 6.337 1.188 1.00 0.00 H ATOM 29 HB2 PRO 3 5.212 7.661 1.568 1.00 0.00 H ATOM 30 HG1 PRO 3 5.571 5.654 3.367 1.00 0.00 H ATOM 31 HG2 PRO 3 3.945 6.303 3.076 1.00 0.00 H ATOM 32 HD1 PRO 3 5.175 3.804 1.803 1.00 0.00 H ATOM 33 HD2 PRO 3 3.599 3.952 2.629 1.00 0.00 H ATOM 34 N ALA 4 5.499 7.083 -1.656 1.00 0.00 N ATOM 35 CA ALA 4 6.262 7.165 -2.905 1.00 0.00 C ATOM 36 CB ALA 4 5.416 6.725 -4.094 1.00 0.00 C ATOM 37 C ALA 4 6.738 8.618 -3.177 1.00 0.00 C ATOM 38 OXT ALA 4 7.513 8.768 -4.161 1.00 0.00 O1- ATOM 39 O ALA 4 6.290 9.477 -2.354 1.00 0.00 O ATOM 40 H ALA 4 5.250 8.002 -1.288 1.00 0.00 H ATOM 41 HA ALA 4 7.137 6.512 -2.806 1.00 0.00 H ATOM 42 HB1 ALA 4 4.539 7.372 -4.215 1.00 0.00 H ATOM 43 HB2 ALA 4 5.988 6.759 -5.027 1.00 0.00 H ATOM 44 HB3 ALA 4 5.053 5.700 -3.965 1.00 0.00 H TER 45 ALA 4 END On 8 October 2015 at 14:15, Dries Van Rompaey wrote: I definitely agree that it's odd that the warning only occurs with this specific residue. I ran a diff against the freshly downloaded AMBER03 files, but they were identical. I also tried running it again with freshly downloaded amber03 files in the directory. About the error: pdb2gmx never crashed. It always runs to completion and mentions that the topology was successfully generated. I only get a warning during the execution of pdb2gmx. Thanks for all your help, Dries On 8 October 2015 at 13:33, Justin Lemkul wrote: On 10/8/15 1:54 AM, Dries Van Rompaey wrote: Thanks for the reply Justin. I unfortunately cannot currently disclose the files that I'm working on. Based on the info presented, would you say that it's an issue with the force field definition or with the actual protein topology? I am not planning on using amber03 in my simulations at the moment, so this specific warning is not that important, but I can't hel
Re: [gmx-users] pdb2gmx error
I did some more testing, it seems that this only occurs when the PRO residue is preceded by a glycine. Could this be related to this issue: http://comments.gmane.org/gmane.science.biology.gromacs.user/72687 ? When I change the glycine residue to anything else, pdb2gmx works like a charm. I constructed a simple test system in which I can replicate the error (see below). REMARK 99 MOE v2014.09 (Chemical Computing Group Inc.) Thu Oct 15 10:05:39 2015 ATOM 1 N ALA 1 0.268 -1.146 -1.547 1.00 0.00 N1+ ATOM 2 CA ALA 1 0.506 0.327 -1.714 1.00 0.00 C ATOM 3 CB ALA 1 -0.837 1.004 -1.931 1.00 0.00 C ATOM 4 C ALA 1 1.226 0.877 -0.480 1.00 0.00 C ATOM 5 O ALA 1 1.399 0.165 0.509 1.00 0.00 O ATOM 6 H1 ALA 1 -0.272 -1.324 -0.688 1.00 0.00 H ATOM 7 H2 ALA 1 -0.224 -1.571 -2.343 1.00 0.00 H ATOM 8 H3 ALA 1 1.161 -1.641 -1.413 1.00 0.00 H ATOM 9 HA ALA 1 1.151 0.435 -2.592 1.00 0.00 H ATOM 10 HB1 ALA 1 -1.364 0.570 -2.788 1.00 0.00 H ATOM 11 HB2 ALA 1 -1.480 0.906 -1.049 1.00 0.00 H ATOM 12 HB3 ALA 1 -0.710 2.074 -2.125 1.00 0.00 H ATOM 13 N GLY 2 1.667 2.171 -0.583 1.00 0.00 N ATOM 14 CA GLY 2 2.390 2.835 0.493 1.00 0.00 C ATOM 15 C GLY 2 2.792 4.221 0.005 1.00 0.00 C ATOM 16 O GLY 2 2.258 4.706 -0.997 1.00 0.00 O ATOM 17 H GLY 2 1.519 2.744 -1.415 1.00 0.00 H ATOM 18 HA1 GLY 2 1.730 2.918 1.361 1.00 0.00 H ATOM 19 HA2 GLY 2 3.269 2.234 0.743 1.00 0.00 H ATOM 20 N PRO 3 3.764 4.872 0.730 1.00 0.00 N ATOM 21 CD PRO 3 4.331 4.472 2.006 1.00 0.00 C ATOM 22 CG PRO 3 4.793 5.786 2.610 1.00 0.00 C ATOM 23 CB PRO 3 5.270 6.581 1.399 1.00 0.00 C ATOM 24 CA PRO 3 4.347 6.129 0.260 1.00 0.00 C ATOM 25 C PRO 3 5.168 5.908 -1.021 1.00 0.00 C ATOM 26 O PRO 3 5.520 4.796 -1.412 1.00 0.00 O ATOM 27 HA PRO 3 3.538 6.843 0.069 1.00 0.00 H ATOM 28 HB1 PRO 3 6.318 6.337 1.188 1.00 0.00 H ATOM 29 HB2 PRO 3 5.212 7.661 1.568 1.00 0.00 H ATOM 30 HG1 PRO 3 5.571 5.654 3.367 1.00 0.00 H ATOM 31 HG2 PRO 3 3.945 6.303 3.076 1.00 0.00 H ATOM 32 HD1 PRO 3 5.175 3.804 1.803 1.00 0.00 H ATOM 33 HD2 PRO 3 3.599 3.952 2.629 1.00 0.00 H ATOM 34 N ALA 4 5.499 7.083 -1.656 1.00 0.00 N ATOM 35 CA ALA 4 6.262 7.165 -2.905 1.00 0.00 C ATOM 36 CB ALA 4 5.416 6.725 -4.094 1.00 0.00 C ATOM 37 C ALA 4 6.738 8.618 -3.177 1.00 0.00 C ATOM 38 OXT ALA 4 7.513 8.768 -4.161 1.00 0.00 O1- ATOM 39 O ALA 4 6.290 9.477 -2.354 1.00 0.00 O ATOM 40 H ALA 4 5.250 8.002 -1.288 1.00 0.00 H ATOM 41 HA ALA 4 7.137 6.512 -2.806 1.00 0.00 H ATOM 42 HB1 ALA 4 4.539 7.372 -4.215 1.00 0.00 H ATOM 43 HB2 ALA 4 5.988 6.759 -5.027 1.00 0.00 H ATOM 44 HB3 ALA 4 5.053 5.700 -3.965 1.00 0.00 H TER 45 ALA 4 END On 8 October 2015 at 14:15, Dries Van Rompaey wrote: > I definitely agree that it's odd that the warning only occurs with this > specific residue. I ran a diff against the freshly downloaded AMBER03 > files, but they were identical. I also tried running it again with freshly > downloaded amber03 files in the directory. > > About the error: pdb2gmx never crashed. It always runs to completion and > mentions that the topology was successfully generated. I only get a warning > during the execution of pdb2gmx. > > Thanks for all your help, > > Dries > > > > On 8 October 2015 at 13:33, Justin Lemkul wrote: > >> >> >> On 10/8/15 1:54 AM, Dries Van Rompaey wrote: >> >>> Thanks for the reply Justin. I unfortunately cannot currently disclose >>> the >>> files that I'm working on. Based on the info presented, would you say >>> that >>> it's an issue with the force field definition or with the actual protein >>> topology? I am not planning on using amber03 in my simulations at the >>> moment, so this specific warning is not that important, but I can't help >>> but wonder if this warning means something is off in the topology. >>> >>> >> Given that error, there is no topology produced, so there's not going to >> be a problem with the topology itself. >> >> I'm sorry to say that without your actual files, there's literally >> nothing we can do to diagnose this. You say s
Re: [gmx-users] pdb2gmx error
I definitely agree that it's odd that the warning only occurs with this specific residue. I ran a diff against the freshly downloaded AMBER03 files, but they were identical. I also tried running it again with freshly downloaded amber03 files in the directory. About the error: pdb2gmx never crashed. It always runs to completion and mentions that the topology was successfully generated. I only get a warning during the execution of pdb2gmx. Thanks for all your help, Dries On 8 October 2015 at 13:33, Justin Lemkul wrote: > > > On 10/8/15 1:54 AM, Dries Van Rompaey wrote: > >> Thanks for the reply Justin. I unfortunately cannot currently disclose the >> files that I'm working on. Based on the info presented, would you say that >> it's an issue with the force field definition or with the actual protein >> topology? I am not planning on using amber03 in my simulations at the >> moment, so this specific warning is not that important, but I can't help >> but wonder if this warning means something is off in the topology. >> >> > Given that error, there is no topology produced, so there's not going to > be a problem with the topology itself. > > I'm sorry to say that without your actual files, there's literally nothing > we can do to diagnose this. You say some prolines work with AMBER03 and > others don't, which makes no sense at all. Either the .rtp is sound or it > isn't. Either it is unmodified (which will work) or someone has tampered > with it and broken it. > > If you're not going to use AMBER03 and the topology is produced with other > force fields, then you know you have a problem with a hacked AMBER03 .rtp > file. It should be very straightforward to simply to a diff against the > unmodified version (which you can get by downloading a fresh GROMACS > tarball if you don't already have it). > > -Justin > > > On 7 October 2015 at 23:05, Justin Lemkul wrote: >> >> >>> >>> On 10/7/15 5:03 PM, Dries Van Rompaey wrote: >>> >>> Thanks Justin, that makes sense! I'm wondering why none of the other proline residues triggered that warning though? The same procedure works like a charm with other proteins. >>> Without access to all of the files you're looking at, the best I can do >>> is >>> shrug my shoulders because that doesn't make any sense. Some prolines >>> work >>> and one doesn't? That's just not logical. >>> >>> -Justin >>> >>> >>> On 7 Oct 2015 10:59 pm, "Justin Lemkul" wrote: >>> > On 10/7/15 3:01 PM, Dries Van Rompaey wrote: > > Hi Mark, > >> >> This is Gromacs 5.0.4. This is a non-terminal residue. >> The command line used is: >> gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh) >> I tried this procedure with and without ignh flag. >> As far as I know, specbonds is not in play. >> >> >> Non-terminal proline does not have an amide H. If your force field >> .rtp >> > file claims to use such an atom used in a dihedral (which is what the > error > message tells you is happening), find out who altered the file and > reprimand them :) > > -Justin > > Kind regards, > > Dries >> >> >> On 7 October 2015 at 20:56, Mark Abraham >> wrote: >> >> Hi, >> >> >>> Is it terminal? Are there specbonds in play? What's the GROMACS >>> version? >>> What's your pdb2gmx command line? :-) >>> >>> Mark >>> >>> On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey < >>> dries.vanromp...@gmail.com> >>> wrote: >>> >>> Hi everyone, >>> >>> I'm getting the following warning when I try to run pdb2gmx on my protein structure: WARNING: WARNING: Residue 168 named PRO of a molecule in the input file was >>> >>> mapped to an entry in the topology database, but the atom H used in >>> an >>> interaction of type dihedral in that entry is not found in the input file. >>> >>> Perhaps your atom and/or residue naming needs to be fixed. >>> This warning is only present when I use the AMBER03 forcefield, all other forcefields seem to work fine. I have tried this with both a structure without hydrogens as well as a structure with hydrogens added, both with and without the -ignh flag. I tried looking at the amber03 database files as well as the amber99sb-ildn database files (amber99sb-ildn works just fine), but I could not find any reason why this particular residue would be >>> >>> problematic. pdb2gmx does not find any problems with the other >>> proline >>> residues in the protein (which look identical), so I am puzzled as to what's causing this. The proline residue is: ATO
Re: [gmx-users] pdb2gmx error
On 10/8/15 1:54 AM, Dries Van Rompaey wrote: Thanks for the reply Justin. I unfortunately cannot currently disclose the files that I'm working on. Based on the info presented, would you say that it's an issue with the force field definition or with the actual protein topology? I am not planning on using amber03 in my simulations at the moment, so this specific warning is not that important, but I can't help but wonder if this warning means something is off in the topology. Given that error, there is no topology produced, so there's not going to be a problem with the topology itself. I'm sorry to say that without your actual files, there's literally nothing we can do to diagnose this. You say some prolines work with AMBER03 and others don't, which makes no sense at all. Either the .rtp is sound or it isn't. Either it is unmodified (which will work) or someone has tampered with it and broken it. If you're not going to use AMBER03 and the topology is produced with other force fields, then you know you have a problem with a hacked AMBER03 .rtp file. It should be very straightforward to simply to a diff against the unmodified version (which you can get by downloading a fresh GROMACS tarball if you don't already have it). -Justin On 7 October 2015 at 23:05, Justin Lemkul wrote: On 10/7/15 5:03 PM, Dries Van Rompaey wrote: Thanks Justin, that makes sense! I'm wondering why none of the other proline residues triggered that warning though? The same procedure works like a charm with other proteins. Without access to all of the files you're looking at, the best I can do is shrug my shoulders because that doesn't make any sense. Some prolines work and one doesn't? That's just not logical. -Justin On 7 Oct 2015 10:59 pm, "Justin Lemkul" wrote: On 10/7/15 3:01 PM, Dries Van Rompaey wrote: Hi Mark, This is Gromacs 5.0.4. This is a non-terminal residue. The command line used is: gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh) I tried this procedure with and without ignh flag. As far as I know, specbonds is not in play. Non-terminal proline does not have an amide H. If your force field .rtp file claims to use such an atom used in a dihedral (which is what the error message tells you is happening), find out who altered the file and reprimand them :) -Justin Kind regards, Dries On 7 October 2015 at 20:56, Mark Abraham wrote: Hi, Is it terminal? Are there specbonds in play? What's the GROMACS version? What's your pdb2gmx command line? :-) Mark On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey < dries.vanromp...@gmail.com> wrote: Hi everyone, I'm getting the following warning when I try to run pdb2gmx on my protein structure: WARNING: WARNING: Residue 168 named PRO of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type dihedral in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. This warning is only present when I use the AMBER03 forcefield, all other forcefields seem to work fine. I have tried this with both a structure without hydrogens as well as a structure with hydrogens added, both with and without the -ignh flag. I tried looking at the amber03 database files as well as the amber99sb-ildn database files (amber99sb-ildn works just fine), but I could not find any reason why this particular residue would be problematic. pdb2gmx does not find any problems with the other proline residues in the protein (which look identical), so I am puzzled as to what's causing this. The proline residue is: ATOM 1384 N PRO A 168 274.650 45.241 24.167 1.00180.63 N ATOM 1385 CA PRO A 168 273.508 44.823 23.370 1.00180.63 C ATOM 1386 CD PRO A 168 275.844 45.381 23.346 1.00180.63 C ATOM 1387 CB PRO A 168 274.071 44.405 22.014 1.00180.63 C ATOM 1388 CG PRO A 168 275.381 45.194 21.892 1.00180.63 C ATOM 1389 C PRO A 168 272.551 43.776 23.888 1.00180.63 C ATOM 1390 O PRO A 168 271.478 43.646 23.304 1.00180.63 O Does anyone know what's going on here? Thanks in advance! -- 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. -- == Ju
Re: [gmx-users] pdb2gmx error
Thanks for the reply Justin. I unfortunately cannot currently disclose the files that I'm working on. Based on the info presented, would you say that it's an issue with the force field definition or with the actual protein topology? I am not planning on using amber03 in my simulations at the moment, so this specific warning is not that important, but I can't help but wonder if this warning means something is off in the topology. On 7 October 2015 at 23:05, Justin Lemkul wrote: > > > On 10/7/15 5:03 PM, Dries Van Rompaey wrote: > >> Thanks Justin, that makes sense! I'm wondering why none of the other >> proline residues triggered that warning though? The same procedure works >> like a charm with other proteins. >> > > Without access to all of the files you're looking at, the best I can do is > shrug my shoulders because that doesn't make any sense. Some prolines work > and one doesn't? That's just not logical. > > -Justin > > > On 7 Oct 2015 10:59 pm, "Justin Lemkul" wrote: >> >> >>> >>> On 10/7/15 3:01 PM, Dries Van Rompaey wrote: >>> >>> Hi Mark, This is Gromacs 5.0.4. This is a non-terminal residue. The command line used is: gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh) I tried this procedure with and without ignh flag. As far as I know, specbonds is not in play. Non-terminal proline does not have an amide H. If your force field .rtp >>> file claims to use such an atom used in a dihedral (which is what the >>> error >>> message tells you is happening), find out who altered the file and >>> reprimand them :) >>> >>> -Justin >>> >>> Kind regards, >>> Dries On 7 October 2015 at 20:56, Mark Abraham wrote: Hi, > > Is it terminal? Are there specbonds in play? What's the GROMACS > version? > What's your pdb2gmx command line? :-) > > Mark > > On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey < > dries.vanromp...@gmail.com> > wrote: > > Hi everyone, > >> >> I'm getting the following warning when I try to run pdb2gmx on my >> protein >> structure: >> >> WARNING: WARNING: Residue 168 named PRO of a molecule in the input >> file >> >> was > > mapped to an entry in the topology database, but the atom H used in an >> interaction of type dihedral in that entry is not found in the input >> >> file. > > Perhaps your atom and/or residue naming needs to be fixed. >> >> This warning is only present when I use the AMBER03 forcefield, all >> other >> forcefields seem to work fine. I have tried this with both a structure >> without hydrogens as well as a structure with hydrogens added, both >> with >> and without the -ignh flag. I tried looking at the amber03 database >> files >> as well as the amber99sb-ildn database files (amber99sb-ildn works >> just >> fine), but I could not find any reason why this particular residue >> would >> >> be > > problematic. pdb2gmx does not find any problems with the other proline >> residues in the protein (which look identical), so I am puzzled as to >> what's causing this. >> >> The proline residue is: >> ATOM 1384 N PRO A 168 274.650 45.241 24.167 1.00180.63 >> N >> ATOM 1385 CA PRO A 168 273.508 44.823 23.370 1.00180.63 >> C >> ATOM 1386 CD PRO A 168 275.844 45.381 23.346 1.00180.63 >> C >> ATOM 1387 CB PRO A 168 274.071 44.405 22.014 1.00180.63 >> C >> ATOM 1388 CG PRO A 168 275.381 45.194 21.892 1.00180.63 >> C >> ATOM 1389 C PRO A 168 272.551 43.776 23.888 1.00180.63 >> C >> ATOM 1390 O PRO A 168 271.478 43.646 23.304 1.00180.63 >> O >> >> Does anyone know what's going on here? >> >> Thanks in advance! >> -- >> 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. > > > -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> D
Re: [gmx-users] pdb2gmx error
On 10/7/15 5:03 PM, Dries Van Rompaey wrote: Thanks Justin, that makes sense! I'm wondering why none of the other proline residues triggered that warning though? The same procedure works like a charm with other proteins. Without access to all of the files you're looking at, the best I can do is shrug my shoulders because that doesn't make any sense. Some prolines work and one doesn't? That's just not logical. -Justin On 7 Oct 2015 10:59 pm, "Justin Lemkul" wrote: On 10/7/15 3:01 PM, Dries Van Rompaey wrote: Hi Mark, This is Gromacs 5.0.4. This is a non-terminal residue. The command line used is: gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh) I tried this procedure with and without ignh flag. As far as I know, specbonds is not in play. Non-terminal proline does not have an amide H. If your force field .rtp file claims to use such an atom used in a dihedral (which is what the error message tells you is happening), find out who altered the file and reprimand them :) -Justin Kind regards, Dries On 7 October 2015 at 20:56, Mark Abraham wrote: Hi, Is it terminal? Are there specbonds in play? What's the GROMACS version? What's your pdb2gmx command line? :-) Mark On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey < dries.vanromp...@gmail.com> wrote: Hi everyone, I'm getting the following warning when I try to run pdb2gmx on my protein structure: WARNING: WARNING: Residue 168 named PRO of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type dihedral in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. This warning is only present when I use the AMBER03 forcefield, all other forcefields seem to work fine. I have tried this with both a structure without hydrogens as well as a structure with hydrogens added, both with and without the -ignh flag. I tried looking at the amber03 database files as well as the amber99sb-ildn database files (amber99sb-ildn works just fine), but I could not find any reason why this particular residue would be problematic. pdb2gmx does not find any problems with the other proline residues in the protein (which look identical), so I am puzzled as to what's causing this. The proline residue is: ATOM 1384 N PRO A 168 274.650 45.241 24.167 1.00180.63 N ATOM 1385 CA PRO A 168 273.508 44.823 23.370 1.00180.63 C ATOM 1386 CD PRO A 168 275.844 45.381 23.346 1.00180.63 C ATOM 1387 CB PRO A 168 274.071 44.405 22.014 1.00180.63 C ATOM 1388 CG PRO A 168 275.381 45.194 21.892 1.00180.63 C ATOM 1389 C PRO A 168 272.551 43.776 23.888 1.00180.63 C ATOM 1390 O PRO A 168 271.478 43.646 23.304 1.00180.63 O Does anyone know what's going on here? Thanks in advance! -- 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. -- == 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.
Re: [gmx-users] pdb2gmx error
Thanks Justin, that makes sense! I'm wondering why none of the other proline residues triggered that warning though? The same procedure works like a charm with other proteins. On 7 Oct 2015 10:59 pm, "Justin Lemkul" wrote: > > > On 10/7/15 3:01 PM, Dries Van Rompaey wrote: > >> Hi Mark, >> >> This is Gromacs 5.0.4. This is a non-terminal residue. >> The command line used is: >> gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh) >> I tried this procedure with and without ignh flag. >> As far as I know, specbonds is not in play. >> >> > Non-terminal proline does not have an amide H. If your force field .rtp > file claims to use such an atom used in a dihedral (which is what the error > message tells you is happening), find out who altered the file and > reprimand them :) > > -Justin > > Kind regards, >> Dries >> >> >> On 7 October 2015 at 20:56, Mark Abraham >> wrote: >> >> Hi, >>> >>> Is it terminal? Are there specbonds in play? What's the GROMACS version? >>> What's your pdb2gmx command line? :-) >>> >>> Mark >>> >>> On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey < >>> dries.vanromp...@gmail.com> >>> wrote: >>> >>> Hi everyone, I'm getting the following warning when I try to run pdb2gmx on my protein structure: WARNING: WARNING: Residue 168 named PRO of a molecule in the input file >>> was >>> mapped to an entry in the topology database, but the atom H used in an interaction of type dihedral in that entry is not found in the input >>> file. >>> Perhaps your atom and/or residue naming needs to be fixed. This warning is only present when I use the AMBER03 forcefield, all other forcefields seem to work fine. I have tried this with both a structure without hydrogens as well as a structure with hydrogens added, both with and without the -ignh flag. I tried looking at the amber03 database files as well as the amber99sb-ildn database files (amber99sb-ildn works just fine), but I could not find any reason why this particular residue would >>> be >>> problematic. pdb2gmx does not find any problems with the other proline residues in the protein (which look identical), so I am puzzled as to what's causing this. The proline residue is: ATOM 1384 N PRO A 168 274.650 45.241 24.167 1.00180.63 N ATOM 1385 CA PRO A 168 273.508 44.823 23.370 1.00180.63 C ATOM 1386 CD PRO A 168 275.844 45.381 23.346 1.00180.63 C ATOM 1387 CB PRO A 168 274.071 44.405 22.014 1.00180.63 C ATOM 1388 CG PRO A 168 275.381 45.194 21.892 1.00180.63 C ATOM 1389 C PRO A 168 272.551 43.776 23.888 1.00180.63 C ATOM 1390 O PRO A 168 271.478 43.646 23.304 1.00180.63 O Does anyone know what's going on here? Thanks in advance! -- 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. >>> >>> > -- > == > > 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] pdb2gmx error
On 10/7/15 3:01 PM, Dries Van Rompaey wrote: Hi Mark, This is Gromacs 5.0.4. This is a non-terminal residue. The command line used is: gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh) I tried this procedure with and without ignh flag. As far as I know, specbonds is not in play. Non-terminal proline does not have an amide H. If your force field .rtp file claims to use such an atom used in a dihedral (which is what the error message tells you is happening), find out who altered the file and reprimand them :) -Justin Kind regards, Dries On 7 October 2015 at 20:56, Mark Abraham wrote: Hi, Is it terminal? Are there specbonds in play? What's the GROMACS version? What's your pdb2gmx command line? :-) Mark On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey < dries.vanromp...@gmail.com> wrote: Hi everyone, I'm getting the following warning when I try to run pdb2gmx on my protein structure: WARNING: WARNING: Residue 168 named PRO of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type dihedral in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. This warning is only present when I use the AMBER03 forcefield, all other forcefields seem to work fine. I have tried this with both a structure without hydrogens as well as a structure with hydrogens added, both with and without the -ignh flag. I tried looking at the amber03 database files as well as the amber99sb-ildn database files (amber99sb-ildn works just fine), but I could not find any reason why this particular residue would be problematic. pdb2gmx does not find any problems with the other proline residues in the protein (which look identical), so I am puzzled as to what's causing this. The proline residue is: ATOM 1384 N PRO A 168 274.650 45.241 24.167 1.00180.63 N ATOM 1385 CA PRO A 168 273.508 44.823 23.370 1.00180.63 C ATOM 1386 CD PRO A 168 275.844 45.381 23.346 1.00180.63 C ATOM 1387 CB PRO A 168 274.071 44.405 22.014 1.00180.63 C ATOM 1388 CG PRO A 168 275.381 45.194 21.892 1.00180.63 C ATOM 1389 C PRO A 168 272.551 43.776 23.888 1.00180.63 C ATOM 1390 O PRO A 168 271.478 43.646 23.304 1.00180.63 O Does anyone know what's going on here? Thanks in advance! -- 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. -- == 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] pdb2gmx error
Hi Mark, This is Gromacs 5.0.4. This is a non-terminal residue. The command line used is: gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh) I tried this procedure with and without ignh flag. As far as I know, specbonds is not in play. Kind regards, Dries On 7 October 2015 at 20:56, Mark Abraham wrote: > Hi, > > Is it terminal? Are there specbonds in play? What's the GROMACS version? > What's your pdb2gmx command line? :-) > > Mark > > On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey < > dries.vanromp...@gmail.com> > wrote: > > > Hi everyone, > > > > I'm getting the following warning when I try to run pdb2gmx on my protein > > structure: > > > > WARNING: WARNING: Residue 168 named PRO of a molecule in the input file > was > > mapped to an entry in the topology database, but the atom H used in an > > interaction of type dihedral in that entry is not found in the input > file. > > Perhaps your atom and/or residue naming needs to be fixed. > > > > This warning is only present when I use the AMBER03 forcefield, all other > > forcefields seem to work fine. I have tried this with both a structure > > without hydrogens as well as a structure with hydrogens added, both with > > and without the -ignh flag. I tried looking at the amber03 database files > > as well as the amber99sb-ildn database files (amber99sb-ildn works just > > fine), but I could not find any reason why this particular residue would > be > > problematic. pdb2gmx does not find any problems with the other proline > > residues in the protein (which look identical), so I am puzzled as to > > what's causing this. > > > > The proline residue is: > > ATOM 1384 N PRO A 168 274.650 45.241 24.167 1.00180.63 > > N > > ATOM 1385 CA PRO A 168 273.508 44.823 23.370 1.00180.63 > > C > > ATOM 1386 CD PRO A 168 275.844 45.381 23.346 1.00180.63 > > C > > ATOM 1387 CB PRO A 168 274.071 44.405 22.014 1.00180.63 > > C > > ATOM 1388 CG PRO A 168 275.381 45.194 21.892 1.00180.63 > > C > > ATOM 1389 C PRO A 168 272.551 43.776 23.888 1.00180.63 > > C > > ATOM 1390 O PRO A 168 271.478 43.646 23.304 1.00180.63 > > O > > > > Does anyone know what's going on here? > > > > Thanks in advance! > > -- > > 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. > -- 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] pdb2gmx error
Hi, Is it terminal? Are there specbonds in play? What's the GROMACS version? What's your pdb2gmx command line? :-) Mark On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey wrote: > Hi everyone, > > I'm getting the following warning when I try to run pdb2gmx on my protein > structure: > > WARNING: WARNING: Residue 168 named PRO of a molecule in the input file was > mapped to an entry in the topology database, but the atom H used in an > interaction of type dihedral in that entry is not found in the input file. > Perhaps your atom and/or residue naming needs to be fixed. > > This warning is only present when I use the AMBER03 forcefield, all other > forcefields seem to work fine. I have tried this with both a structure > without hydrogens as well as a structure with hydrogens added, both with > and without the -ignh flag. I tried looking at the amber03 database files > as well as the amber99sb-ildn database files (amber99sb-ildn works just > fine), but I could not find any reason why this particular residue would be > problematic. pdb2gmx does not find any problems with the other proline > residues in the protein (which look identical), so I am puzzled as to > what's causing this. > > The proline residue is: > ATOM 1384 N PRO A 168 274.650 45.241 24.167 1.00180.63 > N > ATOM 1385 CA PRO A 168 273.508 44.823 23.370 1.00180.63 > C > ATOM 1386 CD PRO A 168 275.844 45.381 23.346 1.00180.63 > C > ATOM 1387 CB PRO A 168 274.071 44.405 22.014 1.00180.63 > C > ATOM 1388 CG PRO A 168 275.381 45.194 21.892 1.00180.63 > C > ATOM 1389 C PRO A 168 272.551 43.776 23.888 1.00180.63 > C > ATOM 1390 O PRO A 168 271.478 43.646 23.304 1.00180.63 > O > > Does anyone know what's going on here? > > Thanks in advance! > -- > 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] pdb2gmx error
Hi everyone, I'm getting the following warning when I try to run pdb2gmx on my protein structure: WARNING: WARNING: Residue 168 named PRO of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type dihedral in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. This warning is only present when I use the AMBER03 forcefield, all other forcefields seem to work fine. I have tried this with both a structure without hydrogens as well as a structure with hydrogens added, both with and without the -ignh flag. I tried looking at the amber03 database files as well as the amber99sb-ildn database files (amber99sb-ildn works just fine), but I could not find any reason why this particular residue would be problematic. pdb2gmx does not find any problems with the other proline residues in the protein (which look identical), so I am puzzled as to what's causing this. The proline residue is: ATOM 1384 N PRO A 168 274.650 45.241 24.167 1.00180.63 N ATOM 1385 CA PRO A 168 273.508 44.823 23.370 1.00180.63 C ATOM 1386 CD PRO A 168 275.844 45.381 23.346 1.00180.63 C ATOM 1387 CB PRO A 168 274.071 44.405 22.014 1.00180.63 C ATOM 1388 CG PRO A 168 275.381 45.194 21.892 1.00180.63 C ATOM 1389 C PRO A 168 272.551 43.776 23.888 1.00180.63 C ATOM 1390 O PRO A 168 271.478 43.646 23.304 1.00180.63 O Does anyone know what's going on here? Thanks in advance! -- 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] pdb2gmx error
On 7/26/15 6:46 AM, faride badalkhani wrote: Dear all, could anybody help me at this error? Fatal error: atom N not found in buiding block 1AMC while combining tdb and rtp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Use -ter and select appropriately (probably "None" in the case of a polymer, provided you're following http://www.gromacs.org/Documentation/How-tos/Polymers). If you don't specify terminal patching, pdb2gmx defaults to assuming you want protein-like N- and C-terminal termini. -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.
[gmx-users] pdb2gmx error
Dear all, could anybody help me at this error? Fatal error: atom N not found in buiding block 1AMC while combining tdb and rtp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Kind regards, Farideh -- 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] pdb2gmx error "residue not found in residue topology database"
Thank You Mr. Peter I just checked your response and that really helps. Gaussian allows you to save the file in different format(.pdb inclusive), I just choosed to save in .pdb format. I don’t know if I did the right thing. hahaha... On Jul 9, 2015, at 8:17 PM, su wrote: > Peter, This question was for Ali.H.. 😉 > > Sent from my iPhone > >> On 09-Jul-2015, at 5:20 pm, Peter Stern wrote: >> >> I never did that. >> >> >> -Original Message- >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se >> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of su >> Sent: Wednesday, July 08, 2015 11:26 PM >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] pdb2gmx error "residue not found in residue >> topology database" >> >> How you converted the gaussian file into .pdb? Because once i did the same >> and suffered from some missing co ordinates. >> >> Sent from my iPhone >> >>> On 08-Jul-2015, at 11:16 pm, Peter Stern wrote: >>> >>> Look at the file: residuetypes.dat in the ../top/ directory of your >>> installation. >>> It lists all the residue names and more. >>> >>> Peter Stern >>> Weizmann Institute >>> >>> Sent from my iPad >>> >>>> On 8 ביולי 2015, at 17:45, Hamisu Aliyu Mohd >>>> wrote: >>>> >>>> >>>> Dear gmx-users, >>>> >>>> I am really new in this field of endeavour and I am trying investigate the >>>> solubility of peptides in organic solvents, I built a simple tripeptide >>>> (gly-gly-gly) using Gaussian 5.0 and I convert the output file(.out) to >>>> .pdb. I am now trying to use pdb2gmx tool to generate topology for my >>>> peptide using GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) I was >>>> promoted with an error "residue not found in residue topology database” I >>>> checked GROMACS website at http://www.gromacs.org/Documentation/Errors I >>>> learned the residue must have the same name as in the force field, please >>>> I don’t know the naming convention of this force field please HELP. >>>> >>>> Thanks >>>> Ali H. >>>> Department of Chemistry >>>> University Dutse >>>> >>>> -- >>>> 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. >> -- >> 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. > -- > 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] pdb2gmx error "residue not found in residue topology database"
Peter, This question was for Ali.H.. 😉 Sent from my iPhone > On 09-Jul-2015, at 5:20 pm, Peter Stern wrote: > > I never did that. > > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of su > Sent: Wednesday, July 08, 2015 11:26 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] pdb2gmx error "residue not found in residue topology > database" > > How you converted the gaussian file into .pdb? Because once i did the same > and suffered from some missing co ordinates. > > Sent from my iPhone > >> On 08-Jul-2015, at 11:16 pm, Peter Stern wrote: >> >> Look at the file: residuetypes.dat in the ../top/ directory of your >> installation. >> It lists all the residue names and more. >> >> Peter Stern >> Weizmann Institute >> >> Sent from my iPad >> >>> On 8 ביולי 2015, at 17:45, Hamisu Aliyu Mohd >>> wrote: >>> >>> >>> Dear gmx-users, >>> >>> I am really new in this field of endeavour and I am trying investigate the >>> solubility of peptides in organic solvents, I built a simple tripeptide >>> (gly-gly-gly) using Gaussian 5.0 and I convert the output file(.out) to >>> .pdb. I am now trying to use pdb2gmx tool to generate topology for my >>> peptide using GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) I was >>> promoted with an error "residue not found in residue topology database” I >>> checked GROMACS website at http://www.gromacs.org/Documentation/Errors I >>> learned the residue must have the same name as in the force field, please I >>> don’t know the naming convention of this force field please HELP. >>> >>> Thanks >>> Ali H. >>> Department of Chemistry >>> University Dutse >>> >>> -- >>> 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. > -- > 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. -- 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] pdb2gmx error "residue not found in residue topology database"
I never did that. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of su Sent: Wednesday, July 08, 2015 11:26 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] pdb2gmx error "residue not found in residue topology database" How you converted the gaussian file into .pdb? Because once i did the same and suffered from some missing co ordinates. Sent from my iPhone > On 08-Jul-2015, at 11:16 pm, Peter Stern wrote: > > Look at the file: residuetypes.dat in the ../top/ directory of your > installation. > It lists all the residue names and more. > > Peter Stern > Weizmann Institute > > Sent from my iPad > >> On 8 ביולי 2015, at 17:45, Hamisu Aliyu Mohd >> wrote: >> >> >> Dear gmx-users, >> >> I am really new in this field of endeavour and I am trying investigate the >> solubility of peptides in organic solvents, I built a simple tripeptide >> (gly-gly-gly) using Gaussian 5.0 and I convert the output file(.out) to >> .pdb. I am now trying to use pdb2gmx tool to generate topology for my >> peptide using GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) I was >> promoted with an error "residue not found in residue topology database” I >> checked GROMACS website at http://www.gromacs.org/Documentation/Errors I >> learned the residue must have the same name as in the force field, please I >> don’t know the naming convention of this force field please HELP. >> >> Thanks >> Ali H. >> Department of Chemistry >> University Dutse >> >> -- >> 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. -- 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] pdb2gmx error "residue not found in residue topology database"
How you converted the gaussian file into .pdb? Because once i did the same and suffered from some missing co ordinates. Sent from my iPhone > On 08-Jul-2015, at 11:16 pm, Peter Stern wrote: > > Look at the file: residuetypes.dat in the ../top/ directory of your > installation. > It lists all the residue names and more. > > Peter Stern > Weizmann Institute > > Sent from my iPad > >> On 8 ביולי 2015, at 17:45, Hamisu Aliyu Mohd >> wrote: >> >> >> Dear gmx-users, >> >> I am really new in this field of endeavour and I am trying investigate the >> solubility of peptides in organic solvents, I built a simple tripeptide >> (gly-gly-gly) using Gaussian 5.0 and I convert the output file(.out) to >> .pdb. I am now trying to use pdb2gmx tool to generate topology for my >> peptide using GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) I was >> promoted with an error "residue not found in residue topology database” I >> checked GROMACS website at http://www.gromacs.org/Documentation/Errors I >> learned the residue must have the same name as in the force field, please I >> don’t know the naming convention of this force field please HELP. >> >> Thanks >> Ali H. >> Department of Chemistry >> University Dutse >> >> -- >> 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. -- 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] pdb2gmx error "residue not found in residue topology database"
Look at the file: residuetypes.dat in the ../top/ directory of your installation. It lists all the residue names and more. Peter Stern Weizmann Institute Sent from my iPad > On 8 ביולי 2015, at 17:45, Hamisu Aliyu Mohd wrote: > > > Dear gmx-users, > > I am really new in this field of endeavour and I am trying investigate the > solubility of peptides in organic solvents, I built a simple tripeptide > (gly-gly-gly) using Gaussian 5.0 and I convert the output file(.out) to .pdb. > I am now trying to use pdb2gmx tool to generate topology for my peptide using > GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) I was promoted with an > error "residue not found in residue topology database” I checked GROMACS > website at http://www.gromacs.org/Documentation/Errors I learned the residue > must have the same name as in the force field, please I don’t know the naming > convention of this force field please HELP. > > Thanks > Ali H. > Department of Chemistry > University Dutse > > -- > 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] pdb2gmx error "residue not found in residue topology database"
Dear gmx-users, I am really new in this field of endeavour and I am trying investigate the solubility of peptides in organic solvents, I built a simple tripeptide (gly-gly-gly) using Gaussian 5.0 and I convert the output file(.out) to .pdb. I am now trying to use pdb2gmx tool to generate topology for my peptide using GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) I was promoted with an error "residue not found in residue topology database” I checked GROMACS website at http://www.gromacs.org/Documentation/Errors I learned the residue must have the same name as in the force field, please I don’t know the naming convention of this force field please HELP. Thanks Ali H. Department of Chemistry University Dutse -- 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] pdb2gmx error with addition of terminal group
Thanks Justin. Its working fine. On Wed, Jul 8, 2015 at 12:32 PM, Justin Lemkul wrote: > > > On 7/8/15 6:39 AM, anu chandra wrote: > >> Dear Gromacs users, >> >> I am trying to use pdb2gmx tool to generate topology for my membrane >> protein system with chamrm36 force field. I have downloaded Gromacs >> compatible Chamrmm36ff from >> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs. I build the >> N-terminal acetyl (ACE) and C-terminal N-methyl amide (NMA) group >> attached >> to the respective terminals. As shown below, I have named the residue/atom >> names according to the one present in 'merged.rtp' in the charmm36ff file. >> >> >> *** >> ATOM 1 CH3 ACE 1 37.718 66.293 67.509 1.00 0.00 >> PROA >> ATOM 2 HH31 ACE 1 36.850 66.906 67.178 1.00 0.00 >> PROA >> ATOM 3 HH32 ACE 1 37.393 65.240 67.617 1.00 0.00 >> PROA >> ATOM 4 HH33 ACE 1 38.522 66.381 66.751 1.00 0.00 >> PROA >> ATOM 5 C ACE 1 38.195 66.802 68.805 1.00 0.00 >> PROA >> ATOM 6 O ACE 1 37.657 67.757 69.352 1.00 0.00 >> PROA >> ATOM 7 N VAL 1 39.245 66.166 69.366 1.00 0.00 >> PROA >> ATOM 8 HN VAL 1 39.698 65.409 68.911 1.00 0.00 >> PROA >> ATOM 9 CA VAL 1 39.818 66.600 70.628 1.00 0.00 >> PROA >> ATOM 10 HA VAL 1 39.044 66.557 71.385 1.00 0.00 >> PROA >> >> >> ATOM 2599 HG1 SER 165 47.684 67.280 81.712 1.00 0.00 >> PROA >> ATOM 2600 C SER 165 46.288 64.682 84.443 1.00 0.02 >> PROA >> ATOM 2601 O SER 165 46.621 64.090 85.417 1.00 0.04 >> PROA >> ATOM 2602 N NMA 166 45.020 64.893 84.635 1.00 0.03 >> PROA >> ATOM 2603 HN NMA 166 44.986 65.779 85.049 1.00 0.00 >> PROA >> ATOM 2604 CH3 NMA 166 44.322 63.814 85.342 1.00 0.04 >> PROA >> ATOM 2605 HH31 NMA 166 44.694 62.798 85.066 1.00 0.04 >> PROA >> ATOM 2606 HH32 NMA 166 43.284 63.888 85.004 1.00 0.04 >> PROA >> ATOM 2607 HH33 NMA 166 44.382 63.845 86.467 1.00 0.06 >> PROA >> >> *** >> >> But, when running ' gmx pdb2gmx -f input.pdb -ter' and opting 'none' for >> the terminal, the pogram terminate with following error >> >> >> *** >> Back Off! I just backed up topol.top to ./#topol.top# >> Processing chain 1 (2607 atoms, 167 residues) >> Identified residue ACE1 as a starting terminus. >> Warning: Residue NMA166 in chain has different type (Other) from starting >> residue ACE1 (Protein). >> Identified residue SER165 as a ending terminus. >> 8 out of 8 lines of specbond.dat converted successfully >> Special Atom Distance matrix: >> CYS64 CYS72 CYS95 MET100 CYS101 >>SG1007 SG1123 SG1473 SD1554 SG1568 >> CYS72 SG1123 0.857 >> CYS95 SG1473 2.147 1.806 >>MET100 SD1554 2.390 1.830 0.806 >>CYS101 SG1568 1.896 1.488 0.334 0.773 >>MET143 SD2232 1.844 1.750 1.858 2.389 1.687 >> Select start terminus type for ACE-1 >> 0: NH3+ >> 1: NH2 >> 2: 5TER >> 3: None >> 3 >> Start terminus ACE-1: None >> Select end terminus type for SER-165 >> 0: COO- >> 1: COOH >> 2: CT2 >> 3: 3TER >> 4: None >> 4 >> End terminus SER-165: None >> >> --- >> Program gmx, VERSION 5.0.4 >> Source code file: >> /usr/local/gromacs-5.0.4/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1091 >> >> Fatal error: >> *There is a dangling bond at at least one of the terminal ends. Fix your >> coordinate file, add a new terminal database entry (.tdb), or select the >> proper existing terminal entry.* >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> --- >> >> ** >> >> Can anybody help me to figure out what is wrong with my input pdb file? >> >> > Note that pdb2gmx finds Ser instead of NMA as the last residue. The clue > is: > > " Warning: Residue NMA166 in chain has different type (Other) from > starting residue ACE1 (Protein)" > > You need to add NMA as "Protein" in residuetypes.dat. You don't want a > non-patched terminus on Ser, you want a non-patched terminus on NMA. > > -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 > Univ
Re: [gmx-users] pdb2gmx error with addition of terminal group
On 7/8/15 6:39 AM, anu chandra wrote: Dear Gromacs users, I am trying to use pdb2gmx tool to generate topology for my membrane protein system with chamrm36 force field. I have downloaded Gromacs compatible Chamrmm36ff from http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs. I build the N-terminal acetyl (ACE) and C-terminal N-methyl amide (NMA) group attached to the respective terminals. As shown below, I have named the residue/atom names according to the one present in 'merged.rtp' in the charmm36ff file. *** ATOM 1 CH3 ACE 1 37.718 66.293 67.509 1.00 0.00 PROA ATOM 2 HH31 ACE 1 36.850 66.906 67.178 1.00 0.00 PROA ATOM 3 HH32 ACE 1 37.393 65.240 67.617 1.00 0.00 PROA ATOM 4 HH33 ACE 1 38.522 66.381 66.751 1.00 0.00 PROA ATOM 5 C ACE 1 38.195 66.802 68.805 1.00 0.00 PROA ATOM 6 O ACE 1 37.657 67.757 69.352 1.00 0.00 PROA ATOM 7 N VAL 1 39.245 66.166 69.366 1.00 0.00 PROA ATOM 8 HN VAL 1 39.698 65.409 68.911 1.00 0.00 PROA ATOM 9 CA VAL 1 39.818 66.600 70.628 1.00 0.00 PROA ATOM 10 HA VAL 1 39.044 66.557 71.385 1.00 0.00 PROA ATOM 2599 HG1 SER 165 47.684 67.280 81.712 1.00 0.00 PROA ATOM 2600 C SER 165 46.288 64.682 84.443 1.00 0.02 PROA ATOM 2601 O SER 165 46.621 64.090 85.417 1.00 0.04 PROA ATOM 2602 N NMA 166 45.020 64.893 84.635 1.00 0.03 PROA ATOM 2603 HN NMA 166 44.986 65.779 85.049 1.00 0.00 PROA ATOM 2604 CH3 NMA 166 44.322 63.814 85.342 1.00 0.04 PROA ATOM 2605 HH31 NMA 166 44.694 62.798 85.066 1.00 0.04 PROA ATOM 2606 HH32 NMA 166 43.284 63.888 85.004 1.00 0.04 PROA ATOM 2607 HH33 NMA 166 44.382 63.845 86.467 1.00 0.06 PROA *** But, when running ' gmx pdb2gmx -f input.pdb -ter' and opting 'none' for the terminal, the pogram terminate with following error *** Back Off! I just backed up topol.top to ./#topol.top# Processing chain 1 (2607 atoms, 167 residues) Identified residue ACE1 as a starting terminus. Warning: Residue NMA166 in chain has different type (Other) from starting residue ACE1 (Protein). Identified residue SER165 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS64 CYS72 CYS95 MET100 CYS101 SG1007 SG1123 SG1473 SD1554 SG1568 CYS72 SG1123 0.857 CYS95 SG1473 2.147 1.806 MET100 SD1554 2.390 1.830 0.806 CYS101 SG1568 1.896 1.488 0.334 0.773 MET143 SD2232 1.844 1.750 1.858 2.389 1.687 Select start terminus type for ACE-1 0: NH3+ 1: NH2 2: 5TER 3: None 3 Start terminus ACE-1: None Select end terminus type for SER-165 0: COO- 1: COOH 2: CT2 3: 3TER 4: None 4 End terminus SER-165: None --- Program gmx, VERSION 5.0.4 Source code file: /usr/local/gromacs-5.0.4/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1091 Fatal error: *There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry.* For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- ** Can anybody help me to figure out what is wrong with my input pdb file? Note that pdb2gmx finds Ser instead of NMA as the last residue. The clue is: " Warning: Residue NMA166 in chain has different type (Other) from starting residue ACE1 (Protein)" You need to add NMA as "Protein" in residuetypes.dat. You don't want a non-patched terminus on Ser, you want a non-patched terminus on NMA. -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
[gmx-users] pdb2gmx error with addition of terminal group
Dear Gromacs users, I am trying to use pdb2gmx tool to generate topology for my membrane protein system with chamrm36 force field. I have downloaded Gromacs compatible Chamrmm36ff from http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs. I build the N-terminal acetyl (ACE) and C-terminal N-methyl amide (NMA) group attached to the respective terminals. As shown below, I have named the residue/atom names according to the one present in 'merged.rtp' in the charmm36ff file. *** ATOM 1 CH3 ACE 1 37.718 66.293 67.509 1.00 0.00 PROA ATOM 2 HH31 ACE 1 36.850 66.906 67.178 1.00 0.00 PROA ATOM 3 HH32 ACE 1 37.393 65.240 67.617 1.00 0.00 PROA ATOM 4 HH33 ACE 1 38.522 66.381 66.751 1.00 0.00 PROA ATOM 5 C ACE 1 38.195 66.802 68.805 1.00 0.00 PROA ATOM 6 O ACE 1 37.657 67.757 69.352 1.00 0.00 PROA ATOM 7 N VAL 1 39.245 66.166 69.366 1.00 0.00 PROA ATOM 8 HN VAL 1 39.698 65.409 68.911 1.00 0.00 PROA ATOM 9 CA VAL 1 39.818 66.600 70.628 1.00 0.00 PROA ATOM 10 HA VAL 1 39.044 66.557 71.385 1.00 0.00 PROA ATOM 2599 HG1 SER 165 47.684 67.280 81.712 1.00 0.00 PROA ATOM 2600 C SER 165 46.288 64.682 84.443 1.00 0.02 PROA ATOM 2601 O SER 165 46.621 64.090 85.417 1.00 0.04 PROA ATOM 2602 N NMA 166 45.020 64.893 84.635 1.00 0.03 PROA ATOM 2603 HN NMA 166 44.986 65.779 85.049 1.00 0.00 PROA ATOM 2604 CH3 NMA 166 44.322 63.814 85.342 1.00 0.04 PROA ATOM 2605 HH31 NMA 166 44.694 62.798 85.066 1.00 0.04 PROA ATOM 2606 HH32 NMA 166 43.284 63.888 85.004 1.00 0.04 PROA ATOM 2607 HH33 NMA 166 44.382 63.845 86.467 1.00 0.06 PROA *** But, when running ' gmx pdb2gmx -f input.pdb -ter' and opting 'none' for the terminal, the pogram terminate with following error *** Back Off! I just backed up topol.top to ./#topol.top# Processing chain 1 (2607 atoms, 167 residues) Identified residue ACE1 as a starting terminus. Warning: Residue NMA166 in chain has different type (Other) from starting residue ACE1 (Protein). Identified residue SER165 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS64 CYS72 CYS95 MET100 CYS101 SG1007 SG1123 SG1473 SD1554 SG1568 CYS72 SG1123 0.857 CYS95 SG1473 2.147 1.806 MET100 SD1554 2.390 1.830 0.806 CYS101 SG1568 1.896 1.488 0.334 0.773 MET143 SD2232 1.844 1.750 1.858 2.389 1.687 Select start terminus type for ACE-1 0: NH3+ 1: NH2 2: 5TER 3: None 3 Start terminus ACE-1: None Select end terminus type for SER-165 0: COO- 1: COOH 2: CT2 3: 3TER 4: None 4 End terminus SER-165: None --- Program gmx, VERSION 5.0.4 Source code file: /usr/local/gromacs-5.0.4/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1091 Fatal error: *There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry.* For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- ** Can anybody help me to figure out what is wrong with my input pdb file? Many thanks in advance Anu -- 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] pdb2gmx error
If I got it right I would suggest this. Try removing parts in your overall structure. For example let's say your system has 3 components water, ATP, TPO. Try removing all but water, try pdb2gmx, all but ATP ( like a sim in vacuo ) try once again pdb2gmx. This will make the "troubled" part "visible". As for the error message, this comes up when you are trying to simulate a molecule that is not included in the default molecule entries. So you will have to include it manually. But when you know which part produces the error then it will be much easier. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Saman Shahriyari Sent: Sunday, July 5, 2015 10:06 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] pdb2gmx error Dear Users I am trying to run pdb2gmx (in gromacs 5.0.5 and by 43a1p.ff) on o modeled structure holding ATP, water and TPO as hetero atoms. but I am faced with the following error. I checked all LUE residues (although I have got no residue with 28215089 number) and I found no missing atom N. I am really wondering what should be my next step. could you help me on this? "Fatal error:Residue 28215089 named LEU of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed." Best regardsSaman -- 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] pdb2gmx error
Dear Users I am trying to run pdb2gmx (in gromacs 5.0.5 and by 43a1p.ff) on o modeled structure holding ATP, water and TPO as hetero atoms. but I am faced with the following error. I checked all LUE residues (although I have got no residue with 28215089 number) and I found no missing atom N. I am really wondering what should be my next step. could you help me on this? "Fatal error:Residue 28215089 named LEU of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed." Best regardsSaman -- 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] pdb2gmx error
Dear Users I am trying to run pdb2gmx (in gromacs 5.0.5 and by 43a1p.ff) on o modeled structure holding ATP, water and TPO as hetero atoms. but I am faced with the following error. I checked all LUE residues (although I have got no residue with 28215089 number) and I found no missing atom N. I am really wondering what should be my next step. could you help me on this? "Fatal error:Residue 28215089 named LEU of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed." Best regardsSaman -- 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] pdb2gmx error
On 4/7/15 7:53 AM, Sneha Menon wrote: Dear all, I want to simulate a polymer - triphenylphosphine connected to a polyethylene glycol polymer using the CHARMM36 forcefield. I obtained the parameters of this polymer (resname TPP) using SwissParam. I added this molecule to the forcefield by following all the steps mentioned in : http://www.gromacs.org/Documentation/Hotos/Adding_a_Residue_to_a_Force_Field I want to embed this polymer into a lipid bilayer. I first tried to make a topology file for the polymer using : *pdb2gmx -f file.pdb -o file.gro* However, it showed up the following error: Fatal error: Residue 1 named TPP of a molecule in the input file was mapped to an entry in the topology database, but the atom 16 used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. I compared the .rtp file as well as the input .pdb file for any missing atoms. I could not find any atoms missing or discrepancy in the atom/residue naming. What else could be the problem? You need to provide the relevant snippets of the .rtp and .pdb files. Something is missing or mismatched, otherwise pdb2gmx would not complain. -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.
[gmx-users] pdb2gmx error
Dear all, I want to simulate a polymer - triphenylphosphine connected to a polyethylene glycol polymer using the CHARMM36 forcefield. I obtained the parameters of this polymer (resname TPP) using SwissParam. I added this molecule to the forcefield by following all the steps mentioned in : http://www.gromacs.org/Documentation/Hotos/Adding_a_Residue_to_a_Force_Field I want to embed this polymer into a lipid bilayer. I first tried to make a topology file for the polymer using : *pdb2gmx -f file.pdb -o file.gro* However, it showed up the following error: Fatal error: Residue 1 named TPP of a molecule in the input file was mapped to an entry in the topology database, but the atom 16 used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. I compared the .rtp file as well as the input .pdb file for any missing atoms. I could not find any atoms missing or discrepancy in the atom/residue naming. What else could be the problem? -- 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] pdb2gmx error
Hi, These errors mean exactly what they say. There's a mismatch between your structure file and the residue structure in the database. So you need to look at them both and see what is wrong. Chapter 5 of the manual is your friend. Mark On 19/03/2015 3:17 am, "RJ" wrote: > Dear gmx, > > > I tried to to use pdb2gmx and get this error for 3 to 4 residues. I even > cleaned my crystal structure using Discovery studio/swissviewer which shows > no error on it. I wonder, how do i rectify this problem ? > > > WARNING: WARNING: Residue 1 named MET of a molecule in the input file was > mapped > to an entry in the topology database, but the atom H used in > an interaction of type angle in that entry is not found in the > input file. Perhaps your atom and/or residue naming needs to be > fixed. > > > WARNING: WARNING: Residue 366 named LEU of a molecule in the input file > was mapped > to an entry in the topology database, but the atom O used in > an interaction of type angle in that entry is not found in the > input file. Perhaps your atom and/or residue naming needs to be > fixed. > > > Before cleaning: 7060 pairs > > > Residue 32681 named GLN of a molecule in the input file was mapped > to an entry in the topology database, but the atom N used in > an interaction of type improper in that entry is not found in the > input file. Perhaps your atom and/or residue naming needs to be > fixed. > -- > 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] pdb2gmx error
Dear gmx, I tried to to use pdb2gmx and get this error for 3 to 4 residues. I even cleaned my crystal structure using Discovery studio/swissviewer which shows no error on it. I wonder, how do i rectify this problem ? WARNING: WARNING: Residue 1 named MET of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 366 named LEU of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 7060 pairs Residue 32681 named GLN of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. -- 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.
