[gmx-users] Re: a new GROMACS simulation tool
Sound nice. I would like to try out. Could You please set up an account for me? Regards, Eduardo Villarreal villarea...@hss.edu - Eduardo Villarreal Ramírez Postdoctoral Research Fellow Mineralized Tissue Laboratory, Hospital for Special Surgery. -- View this message in context: http://gromacs.5086.x6.nabble.com/a-new-GROMACS-simulation-tool-tp5011910p5011934.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pdb2gmx takes phosphoserine as terminal ends
Hello Gromacs users, I want to obtain the topology file (topol.top) for this peptide Ace-Ser-Ser-Asp-Sep-Sep-Asp-Sep-Sep-Asp-Sep-Sep-Asp-Sep-Sep-Asp-NH2. I am using this ffG43a1p force field and this command pdb2gmx -f sereno2.pdb -o pep5-dpp-cap-linear-phospho_newbox_up_rotate.gro -ignh -ter -water spc I obtained the next error and warnings: Identified residue ACE1 as a starting terminus. Warning: Residue SEP5 in chain has different type (Other) from starting residue ACE1 (Protein). Warning: Residue SEP6 in chain has different type (Other) from starting residue ACE1 (Protein). Warning: Residue ASP7 in chain has different type (Protein) from starting residue ACE1 (Protein). Warning: Residue SEP8 in chain has different type (Other) from starting residue ACE1 (Protein). Warning: Residue SEP9 in chain has different type (Other) from starting residue ACE1 (Protein). More than 5 unidentified residues at end of chain - disabling further warnings. Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2top.c, line: 1021 Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. According to my pdb file (www.dropbox.com/s/kihycqde78wy787/sereno2.pdb) my peptide is a continuous. I do not know how to figure out this mistake. I will appreciate if someone give me a hint. Thank you in advance, Eduardo - Eduardo Villarreal Ramírez Postdoctoral Research Fellow Mineralized Tissue Laboratory, Hospital for Special Surgery. -- View this message in context: http://gromacs.5086.x6.nabble.com/pdb2gmx-takes-phosphoserine-as-terminal-ends-tp5011684.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: pdb2gmx takes phosphoserine as terminal ends
Dear Justin, Your are right, as usual. Thank you so much. - Eduardo Villarreal Ramírez Postdoctoral Research Fellow Mineralized Tissue Laboratory, Hospital for Special Surgery. -- View this message in context: http://gromacs.5086.x6.nabble.com/pdb2gmx-takes-phosphoserine-as-terminal-ends-tp5011684p5011686.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: ERROR No default G96Angle types
I added this line (CA C Oga_30) to topology file and problem solved. Justin are right as usual, Regards, Eduardo. - Eduardo Villarreal Ramírez Postdoctoral Research Fellow Mineralized Tissue Laboratory, Hospital for Special Surgery. -- View this message in context: http://gromacs.5086.n6.nabble.com/ERROR-No-default-G96Angle-types-tp5006044p5006099.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ERROR No default G96Angle types
Dear Gromacs-Users, I am using Gromos96 43a1 FF extended to include phosphorylated residues. I have a peptide-capped with 17 aminoacids. When I tried to add ions to the virtual box I obtained these error ERROR 1 [file topol.top, line 566]: No default G96Angle types ERROR 2 [file topol.top, line 801]: No default Proper Dih. types The second error was resolved by modified the archive residuetypes.dat. I only add this line SEP Protein To be honest I don't know how to resolve the ERROR 1. If someone could help me I will appreciate. Eduardo grompp -f ions.mdp -c newbox_solv.gro -p topol.top -o ions.tpr ERROR 1 [file topol.top, line 566]: No default G96Angle types topol.top [ angles ] ; aiajak functc0c1c2 c3 1 2 3 2 newbox_solc.gro 1ACE CA1 2.759 1.040 1.830 1ACE C2 2.881 1.130 1.839 1ACE O3 2.988 1.083 1.878 2SER N4 2.872 1.258 1.805 aminoacids.rtp [ ACE ] [ atoms ] CA CH3 0.000 0 C C 0.380 1 O O -0.380 1 [ bonds ] CCA gb_26 C O gb_4 C+N gb_9 [ angles ] CA C+Nga_18 O C+Nga_32 [ impropers ] CCA+N Ogi_1 ERROR 2 [file topol.top, line 801]: No default Proper Dih. types topol.top [ dihedrals ] ; aiajakal functc0c1c2 c3c4c5 72717374 1 H N CACB newbox_sol.gro 10SEP N 71 2.348 2.562 2.883 10SEP H 72 2.446 2.556 2.863 10SEP CA 73 2.260 2.594 2.768 10SEP CB 74 2.186 2.467 2.720 10SEP OG 75 2.110 2.424 2.827 10SEP P 76 2.001 2.314 2.797 10SEPO1P 77 2.066 2.200 2.732 10SEPO2P 78 1.949 2.275 2.928 10SEPO3P 79 1.895 2.372 2.710 10SEP C 80 2.164 2.714 2.789 10SEP O 81 2.051 2.714 2.741 aminoacids.rtp [ SEP ]tar -zcvf prog-1-jan-2005.tar.gz /home/jerry/prog [ atoms ] N N-0.28000 0 H H 0.28000 0 CA CH1 0.0 1 CB CH2 0.0 2 OGOA-0.36000 2 P P 0.94000 2 O1POP-0.86000 2 O2POP-0.86000 2 O3POP-0.86000 2 C C 0.380 3 O O -0.380 3 [ bonds ] N Hgb_2 NCAgb_20 CA Cgb_26 C Ogb_4 C+Ngb_9 CACBgb_26 CBOGgb_17 OG Pgb_27 P O1Pgb_23 P O2Pgb_23 P O3Pgb_23 [ angles ] ; aiajak gromos type -C N H ga_31 H NCA ga_17 -C NCA ga_30 NCA C ga_12 CA C+N ga_18 CA C O ga_29 O C+N ga_32 NCACB ga_12 CCACB ga_12 CACBOG ga_12 CBOG P ga_25 OG P O1P ga_13 OG P O2P ga_13 OG P O3P ga_13 O1P P O2P ga_28 O1P P O3P ga_28 O2P P O3P ga_28 [ impropers ] ; aiajakal gromos type N-CCA H gi_1 CCA+N O gi_1 CA N CCB gi_2 [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_4 -C NCA C gd_19 NCA C+N gd_20 NCACBOG gd_17 CACBOG P gd_14 CBOG P O1P gd_11 - Eduardo Villarreal Ramírez Postdoctoral Research Fellow Mineralized Tissue Laboratory, Hospital for Special Surgery. -- View this message in context: http://gromacs.5086.n6.nabble.com/ERROR-No-default-G96Angle-types-tp5006044.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
