Thanks for Your suggestion, I will use an updated forcefield & gradually adjust each error lines.
Jit On Fri, Feb 12, 2010 at 6:50 PM, Justin A. Lemkul <[email protected]> wrote: > > > chiloo777 777 wrote: >> >> So, I've changed forcefield from ffG53a6 to ffgmx, the errors are as >> following lines. >> Please suggest me, how can i remove such errors. >> > > Well, an arbitrary change to a deprecated force field just to get around a > simple atom type mismatch may or may not be the best way to handle > things...be sure you can justify your use of this outdated force field. If > your justification is "to make errors go away," be sure you're ready for > reviewer criticism. There have been many lively and informative debates > over this list (some in recent weeks) about which parameter sets should and > should not be used for membrane protein simulation, so I would encourage you > to do a few minutes of searching in the archives. > >> 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 >> > > As I said before, look up what's on this line, see what atoms it corresponds > to, and try to figure out why the error is coming up. The line number in > the file is even printed for you, you just have to map back which atoms are > affected. > > -Justin > >> 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 >>> >> >> >> > > -- > ======================================== > > 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
