Hi Justin: Back from the Austrian mountains, to further isolate problems I encountered before with my protein, I have tried to reproduce - at the lowest stage - the CG tutorial for ubiquitin which is provided on the MARTINI web page. I encountered the same problem as with my protein.
I started from files provided in /output.exercises/protein/protein_data/ubiquitin, i.e.: martini_v2.1.itp cg.gro cg.itp cg.top protein-in-vacuum.mdp I commented out all W in cg.top. At the command $ grompp -np 4 -f protein-in-vacuum.mdp -c cg.gro -p cg.top -o cg.tpr Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... WARNING 1 [file protein-in-vacuum.mdp, line unknown]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb/rvdw. calling /lib/cpp... processing topology... Generated 0 of the 465 non-bonded parameter combinations Excluding 1 bonded neighbours for Protein 1 processing coordinates... Warning: atom names in cg.top and cg.gro don't match (BCQd - BN0) Warning: atom names in cg.top and cg.gro don't match (SCC5 - SC1) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEP4 - SC1) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEAC1 - SC1) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SESC4 - SC1) Warning: atom names in cg.top and cg.gro don't match (SESC4 - SC2) Warning: atom names in cg.top and cg.gro don't match (SESC4 - SC3) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEAC2 - SC1) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEC3 - SC1) Warning: atom names in cg.top and cg.gro don't match (SEQd - SC2) Warning: atom names in cg.top and cg.gro don't match (BENda - BN0) Warning: atom names in cg.top and cg.gro don't match (SEP1 - SC1) Warning: atom names in cg.top and cg.gro don't match (BTNda - BN0) Warning: atom names in cg.top and cg.gro don't match (STAC1 - SC1) Warning: atom names in cg.top and cg.gro don't match (BTNda - BN0) (more than 20 non-matching atom names) WARNING 2 [file "cg.top", line 22]: 163 non-matching atom names atom names from cg.top will be used atom names from cg.gro will be ignored double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # BONDS: 160 # G96ANGLES: 161 # PDIHS: 9 # IDIHS: 4 # CONSTR: 30 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /usr/share/gromacs/top/aminoacids.dat There are: 0 OTHER residues There are: 76 PROTEIN residues There are: 0 DNA residues Analysing Protein... ------------------------------------------------------- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/kernel/readir.c, line: 798 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. ================= >From the name "protein-in-vacuum.mdp" I assume that there is no "HOH" around in such file. Also, the tutorial was not for other non-protein. I would be very grateful to the kind person who points out where I did wrongly. Attached is also the mdout.mdp file. thanks francesco pietra On Mon, Oct 5, 2009 at 11:14 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Francesco Pietra wrote: > >>> 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 >> > > This comes up because you've defined one group now for T-coupling and > assigned coupling constants and temperatures for two. Haphazard changes to > .mdp files will certainly generate these errors. Deleting until the problem > goes away never works - it only creates more problems :) > > Please see the manual for proper use of tc-grps, etc. > >>>> 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. >> > > What is "standard" for one user is not necessarily "standard" for another. > You must almost always make changes to suit your particular system, as a > general rule. > >> Thanks for all you did for me (for us) >> > > You're welcome. Hopefully everything works out. > > -Justin > >> 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 >>> >>> >> > > -- > ======================================== > > 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 > >
#mdout.mdp.1#
Description: Binary data
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