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?
Thanks Jit 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 > -- 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
