Re: [gmx-users] Error in generating DPPC using grompp
P1 0.000 3.138 2 CS1 OA1 0.000 1.255 3 CS1 NR5*1 0.000 0.000 2 CS1 CH21 0.000 5.858 3 CS1 OS1 0.000 3.766 3 ; CS1 CS11 0.000 5.858 3 ; CS1 CS11 0.000 0.418 2 ; CS1 CS11 0.000 2.092 2 NR6 CB1 180.000 33.472 2 NR6 CHE1 180.000 33.472 2 NR6* CH21 0.000 0.418 6 NR6* CB1 180.000 33.472 2 NR6* CHE1 180.000 33.472 2 NR6* CS11 0.000 0.000 2 CS2 OA1 0.000 1.255 3 CS2 OS1 0.000 3.766 3 ; CS2 CS11 0.000 5.858 3 ; CS2 CS11 0.000 0.418 2 ; CS2 CS11 0.000 2.092 2 SI CH11 0.000 5.858 3 SI OS1 0.000 3.766 3 C CP21 0.000 0.418 6 CH1 OS1 0.000 3.766 3 C OS1 0.000 3.766 3 CP2 CP21 0.000 0.418 6 [ dihedraltypes ] CP2 CP23 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 CH2 CH23 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 LP2 LP23 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 LH2 LH23 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 #define ANG_180_0 180 0 #define DIH_0_0_2 0 0 2 [DPPC] [atoms] Here you're including an .rtp entry in the topology that should hold only bonded parameters. This is where the error originates; you've pasted together two entirely different files. -Justin C1 CH3 0.124 0 C2 CH3 0.124 0 C3 CH3 0.124 0 N4NL 0.004 0 C5 CH2 0.124 0 C6 CH2 0.000 1 O7OS -0.180 2 P8 P 0.500 2 O9OM -0.320 2 O10OM -0.320 2 O11OS -0.180 2 C12 CH2 0.000 3 C13 CH1 0.100 4 O14OS -0.180 4 C15 C 0.270 4 O16 O -0.190 4 C17 CH2 0.000 5 C18 CH2 0.000 6 C19 CH2 0.000 7 C20 CH2 0.000 8 C21 CH2 0.000 9 C22 CH2 0.00010 C23 CH2 0.00011 C24 CH2 0.00012 C25 CH2 0.00013 ... . .. [ bonds ] C1N4 gb_21 C2N4 gb_21 C3N4 gb_21 N4C5 gb_21 C5C6 gb_27 C6O7 gb_18 O7P8 gb_28 P8O9 gb_24 P8 O10 gb_24 P8 O11 gb_28 . .. [ angles ] ; aiajak gromos type O33N4 C34 ga_13 O33N4 O35 ga_13 O33N4 C32 ga_13 C34N4 O35 ga_13 C34N4 C32 ga_13 O35N4 C32 ga_13 N4 C32 C31 ga_15 C32 C31 C32 ga_15 C31 C32P8 ga_26 C32 P8 O33 ga_14 C32 P8 C34 ga_14 C32 P8 C31 ga_5 O33P8 C34 ga_29 O33P8 C31 ga_14 C34P8 C31 ga_14 P8 C31C3 ga_26 C31C3C2 ga_15 C3C2 C21 ga_13 . ... [ impropers ] ; aiajakal gromos type C13O14 C32 C12 gi_2 C15O14 C17 O16 gi_1 C34O33 C36 O35 gi_1 [ dihedrals ] ; aiajakal gromos type O33N4 C32 C31 gd_29 N4 C32 C31 C32 gd_4 N4 C32 C31 C32 gd_36 C32 C31 C32P8 gd_29 C31 C32P8 C31 gd_20 C31 C32P8 C31 gd_27 C32P8 C31C3 gd_20 C32P8 C31C3 gd_27 P8 C31C3C2 gd_29 ... .. Date: Fri, 21 Jan 2011 06:53:42 -0500 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error in generating DPPC using grompp shobana visolingam wrote: dear all, i am new to gromacs and i'm trying to run the command grompp -c lipo1grobox.pdb -p topol.top -f em_restraints.mdp -o em_restraints.tpr. however i got this error *Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp ERROR 1 [file ffgmxbon_lipid.itp, line 756]: Invalid directive DPPC --- Program grompp, VERSION 4.0.4 Source code file: topio.c, line: 415 Fatal error: Syntax error - File ffgmxbon_lipid.itp, line 757 Last line read: '[atoms]' Invalid order for directive atoms* can i know what this error mean and how to overcome it?? thanks
[gmx-users] Error in generating DPPC using grompp
dear all, i am new to gromacs and i'm trying to run the command grompp -c lipo1grobox.pdb -p topol.top -f em_restraints.mdp -o em_restraints.tpr. however i got this error Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp ERROR 1 [file ffgmxbon_lipid.itp, line 756]: Invalid directive DPPC --- Program grompp, VERSION 4.0.4 Source code file: topio.c, line: 415 Fatal error: Syntax error - File ffgmxbon_lipid.itp, line 757 Last line read: '[atoms]' Invalid order for directive atoms can i know what this error mean and how to overcome it?? thanks. -- 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
Re: [gmx-users] Error in generating DPPC using grompp
shobana visolingam wrote: dear all, i am new to gromacs and i'm trying to run the command grompp -c lipo1grobox.pdb -p topol.top -f em_restraints.mdp -o em_restraints.tpr. however i got this error *Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp ERROR 1 [file ffgmxbon_lipid.itp, line 756]: Invalid directive DPPC --- Program grompp, VERSION 4.0.4 Source code file: topio.c, line: 415 Fatal error: Syntax error - File ffgmxbon_lipid.itp, line 757 Last line read: '[atoms]' Invalid order for directive atoms* can i know what this error mean and how to overcome it?? thanks. You have serious errors in your topology. Without seeing it, there's nothing else anyone can really suggest except for having a thorough read through Chapter 5. The topology must follow a specific order, which you likely have not followed. A simple DPPC topology is available as part of my membrane protein tutorial: http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
