Hi, I wrote an entry in the rtp file of the force field OPLS-AA + Berger lipid parameters
[ DMPC ] [ atoms ] ; ai Ber_type charge resnr mass CN1 LC3 0.4000 1 15.0350 CN2 LC3 0.4000 1 15.0350 CN3 LC3 0.4000 1 15.0350 NTM LNL -0.5000 1 14.0067 CA LH2 0.3000 1 14.0270 CB LC2 0.4000 1 14.0270 OA LOS -0.8000 1 15.9994 P LP 1.7000 1 30.9738 OB LOM -0.8000 1 15.9994 OC LOM -0.8000 1 15.9994 OD LOS -0.7000 1 15.9994 [ bonds ] ; ai aj funct c0 c1 CN1 NTM 2 0.1470 8.7100e+06 CN2 NTM 2 0.1470 8.7100e+06 CN3 NTM 2 0.1470 8.7100e+06 NTM CA 2 0.1470 8.7100e+06 CA CB 2 0.1530 7.1500e+06 CB OA 2 0.1430 8.1800e+06 OA P 2 0.1610 4.8400e+06 P OB 2 0.1480 8.6000e+06 P OC 2 0.1480 8.6000e+06 P OD 2 0.1610 4.8400e+06 OD CC 2 0.1430 8.1800e+06 [ angles ] ; ai aj ak funct angle fc CN1 NTM CN2 2 109.50 520.00 CN1 NTM CN3 2 109.50 520.00 CN1 NTM CA 2 109.50 520.00 CN2 NTM CN3 2 109.50 520.00 CN2 NTM CA 2 109.50 520.00 CN3 NTM CA 2 109.50 520.00 NTM CA CB 2 111.00 530.00 CA CB OA 2 111.00 530.00 CB OA P 2 120.00 530.00 OA P OC 2 109.60 450.00 OA P OB 2 109.60 450.00 OA P OD 2 103.00 420.00 [ dihedrals ] ; ai aj ak al funct ph0 cp mult CN3 NTM CA CB 1 0.00 3.77 3 NTM CA CB OA 1 0.00 8.62 3 CA CB OA P 1 0.00 3.77 3 CB OA P OD 1 0.00 3.19 3 OA P OD CC 1 0.00 3.19 3 P OD CC CD 1 0.00 3.77 3 OD CC CD CE 1 0.00 5.92 3 CC CD OE C1A 1 0.00 3.77 3 CC CD CE OG 1 0.00 5.92 3 CD OE C1A C1B 1 180.00 24.00 2 [ impropers ] ; GROMOS improper dihedrals ; ai aj ak al funct angle fc ; CD OE CE CC 2 35.26 334.72 C1A OE OF C1B 2 0.00 167.36 C2A OG OH C2B 2 0.00 167.36 I got a conf.gro file by using merge command pdb2gmx -f system.pdb -merge all Some part of the output file from above command 262TYR O 2500 2.592 4.761 10.187 263GLY N 2501 2.782 4.734 10.302 263GLY H 2502 2.879 4.719 10.299 263GLY CA 2503 2.716 4.747 10.431 263GLY HA1 2504 2.787 4.723 10.509 263GLY HA2 2505 2.635 4.677 10.435 263GLY C 2506 2.663 4.886 10.455 263GLY O1 2507 2.645 4.925 10.570 263GLY O2 2508 2.640 4.967 10.361 264ZN ZN 2509 4.326 3.894 9.500 265ZN ZN 2510 4.221 3.718 8.159 266CA CA 2511 4.917 3.016 8.702 267CA CA 2512 3.073 4.064 8.337 268CA CA 2513 4.476 2.192 8.391 1DMPC CN1 2514 4.712 3.345 3.963 1DMPC CN2 2515 4.507 3.298 4.076 1DMPC CN3 2516 4.587 3.524 4.058 1DMPC NTM 2517 4.576 3.394 3.989 1DMPC CA 2518 4.511 3.404 3.857 1DMPC CB 2519 4.465 3.280 3.780 1DMPC OA 2520 4.576 3.195 3.752 1DMPC P 2521 4.533 3.055 3.686 1DMPC OB 2522 4.421 2.996 3.764 1DMPC OC 2523 4.528 3.081 3.540 Now I'm trying to execute command to get ions.tpr file >> grompp -f minim.mdp -c conf_solv.gro -p topol.top -o ions.tpr Error encountered was: ------------------------------------------------------ Program g_grompp, VERSION 4.5.5 Source code file: /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c, line: 1631 Fatal error: Incorrect number of parameters - found 3, expected 2 or 4 for Bond. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- I tried to look all the parameters in the .rtp file and ffbonded.itp and ffnonbonded.itp files I don't find any mistake. I hope you can help me --Thanks Rama --------------------------------------------------------------------------------==================== On Wed, Sep 11, 2013 at 9:16 AM, Rama Krishna Koppisetti < ramkishn...@gmail.com> wrote: > Sorry.., Justin > > Yes.. It is a sequence of atom numbers from DMPC atoms. The errors are > coming from all DMPC atoms dihedrals only not by protein dihedrals. > > --Rama > > > On Wed, Sep 11, 2013 at 9:08 AM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 9/11/13 10:06 AM, Rama Krishna Koppisetti wrote: >> >>> Those lines are related to DMPC lipid dihedrals. >>> >>> >> I know that much. I am trying to extract some actual detail here so I >> can help you reach a conclusion. The error indicates line numbers in the >> topology. On those line numbers are a sequence of atom numbers, which can >> be mapped back to atom types. I'm asking you what that specific >> information is. >> >> -Justin >> >> On Wed, Sep 11, 2013 at 8:17 AM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>>> >>>> On 9/11/13 9:05 AM, Rama Krishna Koppisetti wrote: >>>> >>>> Hi Justin, >>>>> >>>>> Should I use R-B dihedrals for DMPC lipids rather than periodic >>>>> dihedrals. >>>>> >>>>> >>>>> You should use whatever the force field tells you. >>>> >>>> >>>> I'm getting an Error message like, >>>> >>>>> >>>>> ERROR 18815 [file topol.top, line 54180]: >>>>> No default Ryckaert-Bell. types >>>>> >>>>> >>>>> ERROR 18816 [file topol.top, line 54181]: >>>>> No default Ryckaert-Bell. types >>>>> >>>>> >>>>> What are the dihedrals on these lines? >>>> >>>> >>>> -Justin >>>> >>>> -- >>>> ==============================****==================== >>>> >>>> >>>> Justin A. Lemkul, Ph.D. >>>> Postdoctoral Fellow >>>> >>>> Department of Pharmaceutical Sciences >>>> School of Pharmacy >>>> Health Sciences Facility II, Room 601 >>>> University of Maryland, Baltimore >>>> 20 Penn St. >>>> Baltimore, MD 21201 >>>> >>>> jalemkul@outerbanks.umaryland.****edu <jalemkul@outerbanks.** >>>> umaryland.edu <jalem...@outerbanks.umaryland.edu>> | (410) >>>> 706-7441 >>>> >>>> ==============================****==================== >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>> > >>>> * Please search the archive at http://www.gromacs.org/** >>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>>> Mailing_Lists/Search<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<http://www.gromacs.org/**Support/Mailing_Lists> >>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>> > >>>> >>>> >> -- >> ==============================**==================== >> >> Justin A. Lemkul, Ph.D. >> Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 601 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu>| >> (410) >> 706-7441 >> >> ==============================**==================== >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >> > > -- gmx-users mailing list gmx-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