So, I've changed forcefield from ffG53a6 to ffgmx, the errors are as following lines. Please suggest me, how can i remove such errors.
Thanks Jit Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/top/ffgmxnb.itp Opening library file /usr/local/gromacs/share/top/ffgmxbon.itp Opening library file /usr/local/gromacs/share/top/ff_dum.itp Generated 1174 of the 2016 non-bonded parameter combinations ERROR 1 [file /DATA/jit/ff53a6/pope.itp, line 234]: No default Proper Dih. types Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 3 bonded neighbours molecule type 'POPE' Excluding 3 bonded neighbours molecule type 'DPOPG' Excluding 3 bonded neighbours molecule type 'LPOPG' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 1 bonded neighbours molecule type 'Na' NOTE 1 [file ../topol.top, line 2359]: System has non-zero total charge: 2.600001e+01 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note ------------------------------------------------------- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There was 1 error in input file(s) ------------------------------------------------------- "Disturb the Peace of a John Q Citizen" (Urban Dance Squad) On Fri, Feb 12, 2010 at 2:49 PM, Mark Abraham <[email protected]> wrote: > On 12/02/10 18:17, chiloo777 777 wrote: >> >> If this problem comes from the mismatch forcefield, That mean i should >> change forcefield from ffG53a6 to ffgmx, or find popg.itp (which is >> matched with ffG53a6), right? > > Standard procedure is to choose a forcefield that is known to be able to > model the kind of system you're working on before you do anything else :-) > > Mark > >> On Fri, Feb 12, 2010 at 9:06 AM, Justin A. Lemkul<[email protected]> wrote: >>> >>> >>> chiloo777 777 wrote: >>>> >>>> To see topology, please see the attached files >>>> >>> >>> You're using ffG53a6, per my tutorial, but then if you look within >>> popg.itp, >>> you'll find atom type HO, which is not a recognized type within 53a6 (it >>> is >>> for ffgmx). The proper type is H. The other warnings are probably due >>> to >>> some other similar force field type mismatch. Identify which of these is >>> problematic (grompp should print the line number in the topology), and >>> assign suitable parameters. >>> >>> As for this: >>> >>> ; Include water topology >>> #include "#include "/usr/local/gromacs/share/top/flexspc.itp" >>> >>> I have no idea how that would even work, you don't even have proper >>> closed >>> quotes, but in any case you would only ever need: >>> >>> #include "flexspc.itp" >>> >>> ...although you shouldn't be using a flexible water model for dynamics, >>> anyway. >>> >>> -Justin >>> >>>> Jit >>>> >>>> On Fri, Feb 12, 2010 at 8:45 AM, Justin A. Lemkul<[email protected]> >>>> wrote: >>>>> >>>>> chiloo777 777 wrote: >>>>>> >>>>>> Do you mean i should change the order of #include thing in file.top or >>>>>> something involving pope.itp? >>>>>> I try to change order of #include thing, there is the same error. >>>>>> Do i need to define something like "proper dihedral types" in pope.itp >>>>>> & popg.itp? >>>>>> >>>>> Without seeing your .top it's hard to give any really useful >>>>> information. >>>>> All the bonded parameters for a given lipid should be included within >>>>> the >>>>> relevant .itp file. If it's coming up as "not found" you're either >>>>> using >>>>> the wrong force field, not #including something at all, or your >>>>> topology >>>>> is >>>>> otherwise incorrectly constructed. >>>>> >>>>> -Justin >>>>> >>>>>> Thanks >>>>>> Jit >>>>>> >>>>>> On Fri, Feb 12, 2010 at 8:24 AM, Mark Abraham<[email protected]> >>>>>> wrote: >>>>>>> >>>>>>> On 12/02/10 12:16, chiloo777 777 wrote: >>>>>>>> >>>>>>>> Dear all, >>>>>>>> >>>>>>>> I face some problem during run grompp (see below), the command is >>>>>>>> "grompp -f em.mdp -c ../2add_lipw/b4ion.gro -p ../topol.top -o >>>>>>>> b4ion.tpr" >>>>>>>> >>>>>>>> -Before this process, i've changed the ffG53a6nb.itp& >>>>>>>> ff53Ga6bon.itp >>>>>>>> according to the tutorial >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html) >>>>>>>> >>>>>>>> my topology, you can see the attached files. >>>>>>>> Thanks in advance >>>>>>>> Jit >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -------------------------------------------------------------------------------------------- >>>>>>>> Ignoring obsolete mdp entry 'cpp' >>>>>>>> >>>>>>>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6# >>>>>>>> checking input for internal consistency... >>>>>>>> processing topology... >>>>>>>> Opening library file /usr/local/gromacs/share/top/ff_dum.itp >>>>>>>> Generated 825 of the 2346 non-bonded parameter combinations >>>>>>>> >>>>>>>> ERROR 1 [file /home/jit/Lipid_Bilayers/pope.itp, line 234]: >>>>>>>> No default Proper Dih. types >>>>>>> >>>>>>> If there's no default proper dihedral types defined, then you've >>>>>>> #included >>>>>>> things in a wrong order. >>>>>>> >>>>>>> Mark >>>>>>> >>>>>>>> ------------------------------------------------------- >>>>>>>> Program grompp, VERSION 4.0.7 >>>>>>>> Source code file: toppush.c, line: 947 >>>>>>>> >>>>>>>> Fatal error: >>>>>>>> Atomtype HO not found >>>>>>>> ------------------------------------------------------- >>>>>>>> >>>>>>>> "There's Nothing We Can't Fix, 'coz We Can Do It in the Mix" >>>>>>>> (Indeep) >>>>>>>> >>>>>>>> >>>>>>> -- >>>>>>> gmx-users mailing list [email protected] >>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>>>> Please search the archive at http://www.gromacs.org/search before >>>>>>> posting! >>>>>>> Please don't post (un)subscribe requests to the list. Use the www >>>>>>> interface >>>>>>> or send it to [email protected]. >>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>>>>> >>>>>> >>>>>> >>>>> -- >>>>> ======================================== >>>>> >>>>> 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 list [email protected] >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>> Please search the archive at http://www.gromacs.org/search before >>>>> posting! >>>>> Please don't post (un)subscribe requests to the list. Use the www >>>>> interface >>>>> or send it to [email protected]. >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>>> >>>> >>>> >>>> >>> >>> -- >>> ======================================== >>> >>> 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 list [email protected] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface >>> or send it to [email protected]. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> >> > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Other mails: [email protected] [email protected] [email protected] -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
