On Mon, Oct 5, 2009 at 8:20 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Francesco Pietra wrote: > >> I have now used protein-in-vacuum.mdp from the ubiquitin cg tutorial. > > Which tutorial is that? Can you provide a link?
http://md.chem.rug.nl/~marrink/coarsegrain.html > >> Again grompp complains that "Fatal error: >> Group Non-Protein not found in indexfile. Maybe you have non-default >> goups in your mdp file, while not using the '-n' option of grompp. In >> that case use the '-n' option." (no more complaining about DPPC, now >> more generic non-protein, which increases the confusion) >> >> Having ruled out the .mdp file as responsible for that, it was easy to >> check that both the protein.gro and the protein.itp files only specify >> standard amino acids. >> > > Why have you ruled the .mdp file out? You will probably find the word > "Non-Protein" somewhere in the .mdp file, most likely in T-coupling groups. > If you have a protein in vacuo, the only groups allowed for T-coupling > would be Protein or System, unless you have specifically made some custom > index groups (but you probably don't want to in this case). > > Look at the .mdp file. You will find Non-Protein somewhere. The .mdp I used is not from a tutorial; it is the general purpose - or standard - mdp provided by Martini. It doe not contain the word "protein" The "protein-in-vacuum.mdp from the ubiquitin CG tutoria does contain both "Protein" and "Non-Protein" words. deleting "Non-Protein", the error from running grompp is: Fatal error: Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values > >> I'll settle the matter until I can generate ideas, or be less tired to >> check again for the presence of that mysterious non-protein. The real >> protein contains chloride ion ligands. I have cleared from them before >> starting with CG and anyway no trace of cl CL Cl. >> > > So that has nothing to do with it. > >> Hope to be able to come again here with a solution of this affair. >> > > The best advice - don't blindly use some .mdp file you find because it works > for a tutorial. Read it, read the manual, and make changes based on what > you actually have in your system. I fully agree. Using "protein-in-vacuum.mdp", although attractive because of "vacuum", was a bold adventure. But the standard mdp I used before is declared to be standard, and my protein is standard. As I said, I'll work hard to come out but before I'll take a few days wandering with my Brittany on the Alps. The Tetraonidae will refresh my mind. Thanks for all you did for me (for us) francesco > > -Justin > >> thanks >> francesco >> PS: the protein CG file contains TER lines separating the subunits, >> but the CG .gro file has no TER. >> >> >>> -Justin >>> >>>> ; >>>> ; mod21 | MARTINI 2.1 >>>> ; >>>> >>>> ; Include force field poarameters containing all particle definitions, >>>> ; the interaction matrix, plus the topology for water. >>>> >>>> #include "martini_v2.1.itp" >>>> >>>> ; Then include the file(s) containing the topologies of other >>>> ; molecules present in your system. >>>> >>>> ; #include "martini_v2.0_lipids.itp" >>>> ; #include "martini_v2.0_salt.itp" >>>> >>>> >>>> #include "mod21.itp" >>>> >>>> ; Define a name for your system >>>> >>>> [ system ] >>>> mod21 >>>> >>>> ; Define the composition of your system >>>> ; The molecule names should correspond to those defined in the itp >>>> file(s). >>>> >>>> [ molecules ] >>>> Protein 1 >>>> ; DPPC 128 >>>> ; W 2000 >>>> ; NA+ 20 >>>> ; CL- 20 >>>> >>>> It seems that commenting out ";" is placed correctly. >>>> >>>> I am sincerely sorry to bother you again. >>>> >>>> francesco >>>> >>>> >>>> >>>>>> With command >>>>>> >>>>>> $ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top -n >>>>>> -o mod21.cg.tpr >>>>>> >>>>>> NOTE: >>>>>> System has non-zero total charge: -5.000000e+01 >>>>>> >>>>>> processing coordinates... >>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >>>>>> (BCQd - BN0) >>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >>>>>> (SCAC1 - SC1) >>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >>>>>> (BCP5 - BN0) >>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >>>>>> (SCP1 - SC1) >>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >>>>>> (BSP5 - BN0) >>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >>>>>> (SSAC1 - SC1) >>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >>>>>> (BCP5 - BN0) >>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >>>>>> (SCC3 - SC1) >>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >>>>>> (SCQd - SC2) >>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >>>>>> (BCP5 - BN0) >>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >>>>>> (SCN0 - SC1) >>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >>>>>> (SCQd - SC2) >>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >>>>>> (BHN0 - BN0) >>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >>>>>> (BHNd - BN0) >>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >>>>>> (SHAC1 - SC1) >>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >>>>>> (BHNd - BN0) >>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >>>>>> (SHSC4 - SC2) >>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >>>>>> (SHSP1 - SC1) >>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >>>>>> (SHSC4 - SC3) >>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >>>>>> (SHSC4 - SC4) >>>>>> (more than 20 non-matching atom names) >>>>>> WARNING 2 [file "mod21.cg.top", line 28]: >>>>>> 2875 non-matching atom names >>>>>> atom names from mod21.cg.top will be used >>>>>> atom names from mod21.cg.box.gro will be ignored >>>>>> >>>>>> double-checking input for internal consistency... >>>>>> renumbering atomtypes... >>>>>> converting bonded parameters... >>>>>> # BONDS: 2724 >>>>>> # G96ANGLES: 2860 >>>>>> # PDIHS: 328 >>>>>> # IDIHS: 187 >>>>>> # CONSTR: 745 >>>>>> Walking down the molecule graph to make shake-blocks >>>>>> initialising group options... >>>>>> processing index file... >>>>>> >>>>>> ------------------------------------------------------- >>>>>> Program grompp, VERSION 3.3.3 >>>>>> Source code file: ../../../../src/gmxlib/futil.c, line: 345 >>>>>> >>>>>> File input/output error: >>>>>> index.ndx >>>>>> ========== >>>>>> Non-matching because of the many -S-S- bonds? Why asking about >>>>>> index.ndx? >>>>>> >>>>> Non-matching names occur because MARTINI doesn't assign them correctly >>>>> in >>>>> the initial system setup. Using the .top names is fine. >>>>> >>>>> The I/O error comes from the fact that you have passed the -n flag to >>>>> grompp >>>>> without having index.ndx in the working directory. Note that having an >>>>> index file doesn't necessarily solve your problem; the warning is >>>>> printed >>>>> in >>>>> case you have non-default groups for, e.g., T-coupling or energygrps. >>>>> If >>>>> you have a "moleculetype not found," then you haven't #included the >>>>> .itp >>>>> file and an index file won't save you. >>>>> >>>>> -Justin >>>>> >>>>>> Thanks for help >>>>>> francesco >>>>>> >>>>>> >>>>>> On Mon, Oct 5, 2009 at 12:33 PM, Justin A. Lemkul <jalem...@vt.edu> >>>>>> wrote: >>>>>>> >>>>>>> Francesco Pietra wrote: >>>>>>>> >>>>>>>> Hi: >>>>>>>> >>>>>>>> As I found it difficult to manage solvation - the way I would like - >>>>>>>> with a pore protein (a trimer) partly immersed into a bilayer, I >>>>>>>> started with the protein alone in vacuum, in order to try to fix the >>>>>>>> problems step-by-step. Unfortunately, I can't fix simple problems >>>>>>>> with >>>>>>>> grompp. >>>>>>>> >>>>>>>> 1) Generated mod21.itp from mod21.pdb >>>>>>>> >>>>>>>> 2) Generated mod21.cg.pdb with awk script) >>>>>>>> >>>>>>>> 3) editconf -f mod21.cg.pdb -o mod21.cg.gro >>>>>>>> >>>>>>>> 4) genbox -cp mod21.cg.gro -box 10 17 10 -o mod21.cg.box.gro >>>>>>>> >>>>>>>> 5) grompp -np 4 -f mod21.cg.box.mdp -c mod21.cg.box.gro -p >>>>>>>> mod21.cg.box.top -warnmax 10 >>>>>>>> >>>>>>>> Error: no such moleculetype Protein. >>>>>>>> >>>>>>>> ............................. >>>>>>>> .mdp is merely a renamed martini_v2.0.example.mdp, taking care that >>>>>>>> "cpp = /usr/bin/cpp". >>>>>>>> >>>>>>>> .top was from editing martini_v2.0.example.top and reads (in between >>>>>>>> ===): >>>>>>>> ====== >>>>>>>> ; >>>>>>>> ; mod21 | MARTINI 2.1 >>>>>>>> ; >>>>>>>> >>>>>>>> ; Include force field parameters containing all particle >>>>>>>> definitions, >>>>>>>> ; the interaction matrix, plus the topology for water. >>>>>>>> >>>>>>>> #include "martini_v2.1.itp" >>>>>>>> >>>>>>>> ; Then include the file(s) containing the topologies of other >>>>>>>> ; molecules present in your system. >>>>>>>> >>>>>>>> ; #include "martini_v2.0_lipids.itp" >>>>>>>> ; #include "martini_v2.0_salt.itp" >>>>>>>> >>>>>>>> #include mod21.itp >>>>>>>> >>>>>>> This #include statement has the wrong syntax. See any of the above >>>>>>> for >>>>>>> the >>>>>>> correct way to do it. >>>>>>> >>>>>>> -Justin >>>>>>> >>>>>>> -- >>>>>>> ======================================== >>>>>>> >>>>>>> Justin A. Lemkul >>>>>>> Ph.D. Candidate >>>>>>> ICTAS Doctoral Scholar >>>>>>> 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 gmx-us...@gromacs.org >>>>>>> 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 gmx-users-requ...@gromacs.org. >>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>>>>> >>>>>>> >>>>> -- >>>>> ======================================== >>>>> >>>>> Justin A. Lemkul >>>>> Ph.D. Candidate >>>>> ICTAS Doctoral Scholar >>>>> 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 gmx-us...@gromacs.org >>>>> 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 gmx-users-requ...@gromacs.org. >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>>> >>>>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> 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 gmx-us...@gromacs.org >>> 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 gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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 gmx-us...@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ 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/search before posting! Please don't post (un)subscribe requests to the list. 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