Hi Francesca, The output is written in .pdb format. That's also stated in the help.
Cheers, Tsjerk On Mon, Feb 20, 2012 at 4:05 PM, francesca vitalini <francesca.vitalin...@gmail.com> wrote: > Just one last question Tsjerk, I was trying to load the cg.gro file > obtained with martinize in vmd and the program says it is unable to > load the molecule. the result of the martinize script looks like: > > MODEL 1 > TITLE Protein in water > CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1 > ATOM 1 BB ALA 1 15.063 17.501 13.232 1.00 0.00 > ATOM 2 BB GLU 2 14.568 13.732 14.199 1.00 0.00 > ATOM 3 SC1 GLU 2 17.373 14.208 15.223 1.00 0.00 > TER > ENDMDL > > Does it sound right to you? > Thanks > > > > 2012/2/20 francesca vitalini <francesca.vitalin...@gmail.com>: >> Thank you so much.. Now it is working. I was trying to do it without >> specifying the secondary structure as I'm having problems with the >> do_dssp command. It is not working basically and I have to use pdb2gmx >> to convert into pdb then go to the dssp webpage and create the dssp >> file from there through the pdb. Do you know a fastest way to make it >> work? Thanks >> >> However, my Martini account never worked, don't know why, so I cannot >> post it directly. >> >> 2012/2/20 Tsjerk Wassenaar <tsje...@gmail.com>: >>> Hey Francesca, >>> >>> Now there's a small bug in the program. Sorry about it. We'll put the >>> fixed version on in a bit. The problem arises because you don't >>> specify the secondary structure and pymol is not yet available for >>> doing so. The workaround is to explicitly set the secondary structure >>> to loop, by adding "-ss LLL" on the command line. Thanks for pointing >>> that out. >>> >>> By the way, you might want to post these issues on the Martini forum: >>> http://md.chem.rug.nl/cgmartini/index.php/user-platform/forum >>> It's not exactly Gromacs... >>> >>> Cheers, >>> >>> Tsjerk >>> >>> On Mon, Feb 20, 2012 at 2:34 PM, francesca vitalini >>> <francesca.vitalin...@gmail.com> wrote: >>>> Done while waiting for your e-mail. the error message now says >>>> >>>> INFO Chain termini will be charged >>>> INFO Residues at chain brakes will not be charged >>>> INFO Local elastic bonds will be used for extended regions. >>>> INFO Position restraints will be generated. >>>> WARNING Position restraints are only enabled if -DPOSRES is set in >>>> the MDP file >>>> INFO Read input structure from file. >>>> INFO Input structure is a PDB file. >>>> INFO Found 1 chains: >>>> INFO 1: (Protein), 25 atoms in 3 residues. >>>> INFO Total size of the system: 3 residues. >>>> Traceback (most recent call last): >>>> File "./martinize-1.0.py", line 2415, in <module> >>>> elif options["-pymol"]: >>>> KeyError: '-pymol' >>>> >>>> and the pdb looks like >>>> >>>> TITLE Protein in water >>>> REMARK THIS IS A SIMULATION BOX >>>> CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1 >>>> MODEL 1 >>>> ATOM 1 N ALA 1 15.650 18.630 12.470 1.00 0.00 >>>> ATOM 2 H1 ALA 1 16.142 19.465 12.716 1.00 0.00 >>>> ATOM 3 H2 ALA 1 16.062 18.229 11.652 1.00 0.00 >>>> ATOM 4 H3 ALA 1 14.692 18.849 12.287 1.00 0.00 >>>> ATOM 5 CA ALA 1 15.730 17.670 13.580 1.00 0.00 >>>> ATOM 6 CB ALA 1 15.240 18.220 14.910 1.00 0.00 >>>> ATOM 7 C ALA 1 14.970 16.400 13.180 1.00 0.00 >>>> ATOM 8 O ALA 1 13.880 16.420 12.610 1.00 0.00 >>>> ATOM 9 N GLU 2 15.500 15.310 13.740 1.00 0.00 >>>> ATOM 10 H GLU 2 16.295 15.467 14.326 1.00 0.00 >>>> ATOM 11 CA GLU 2 15.070 13.910 13.610 1.00 0.00 >>>> ATOM 12 CB GLU 2 16.230 12.950 13.880 1.00 0.00 >>>> ATOM 13 CG GLU 2 16.930 13.120 15.230 1.00 0.00 >>>> ATOM 14 CD GLU 2 17.660 14.430 15.540 1.00 0.00 >>>> ATOM 15 OE1 GLU 2 18.650 14.820 14.880 1.00 0.00 >>>> ATOM 16 OE2 GLU 2 17.070 15.190 16.330 1.00 0.00 >>>> ATOM 17 C GLU 2 13.910 13.480 14.500 1.00 0.00 >>>> ATOM 18 O GLU 2 13.760 12.300 14.810 1.00 0.00 >>>> ATOM 19 N GLU 3 13.000 14.410 14.790 1.00 0.00 >>>> ATOM 20 H GLU 3 13.192 15.329 14.446 1.00 0.00 >>>> ATOM 21 CA GLU 3 11.750 14.260 15.550 1.00 0.00 >>>> ATOM 22 CB GLU 3 11.920 13.690 16.960 1.00 0.00 >>>> ATOM 23 C GLU 3 11.190 15.670 15.730 1.00 0.00 >>>> ATOM 24 O1 GLU 3 11.907 16.693 15.192 1.00 0.00 >>>> ATOM 25 O2 GLU 3 10.020 15.787 16.413 1.00 0.00 >>>> TER >>>> >>>> >>>> can you please explain which the problem is to me? >>>> >>>> thanks >>>> >>>> >>>> >>>> 2012/2/20 Tsjerk Wassenaar <tsje...@gmail.com>: >>>>> Hi Francesca, >>>>> >>>>> Given the error, it seems there's still a mismatch between the number >>>>> of atoms and the number indicated. Try converting your structure to >>>>> PDB and use that for coarsegraining. >>>>> >>>> >>>>> Cheers, >>>>> >>>>> Tsjerk >>>>> >>>>> On Mon, Feb 20, 2012 at 2:08 PM, francesca vitalini >>>>> <francesca.vitalin...@gmail.com> wrote: >>>>>> I've changed that but it is still complaining... >>>>>> >>>>>> INFO Chain termini will be charged >>>>>> INFO Residues at chain brakes will not be charged >>>>>> INFO Local elastic bonds will be used for extended regions. >>>>>> INFO Position restraints will be generated. >>>>>> WARNING Position restraints are only enabled if -DPOSRES is set in >>>>>> the MDP file >>>>>> INFO Read input structure from file. >>>>>> INFO Input structure is a GRO file. Chains will be labeled >>>>>> consecutively. >>>>>> Traceback (most recent call last): >>>>>> File "./martinize-1.0.py", line 2306, in <module> >>>>>> for title,atoms,box in frameIterator(inStream): >>>>>> File "./martinize-1.0.py", line 1183, in groFrameIterator >>>>>> atoms = [groAtom(streamIterator.next()) for i in range(natoms)] >>>>>> File "./martinize-1.0.py", line 1170, in groAtom >>>>>> return (S(a[10:15]), S(a[5:10]), I(a[:5]), " ", >>>>>> 10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44])) >>>>>> ValueError: invalid literal for int() with base 10: '2.' >>>>>> >>>>>> >>>>>> >>>>>> 2012/2/20 Tsjerk Wassenaar <tsje...@gmail.com>: >>>>>>> Hi Francesca, >>>>>>> >>>>>>> The problem is that the second line of your gro file indicates there >>>>>>> are 2410 atoms in the file, while there are only 25. Did you manually >>>>>>> remove water? In that case you have to update the number of atoms in >>>>>>> the second line. The error message should be more explanatory though. >>>>>>> >>>>>>> Cheers, >>>>>>> >>>>>>> Tsjerk >>>>>>> >>>>>>> On Mon, Feb 20, 2012 at 1:57 PM, francesca vitalini >>>>>>> <francesca.vitalin...@gmail.com> wrote: >>>>>>>> I was using the one available from the tutorial but now I have >>>>>>>> downloaded the new one and it gives me still an error message like >>>>>>>> >>>>>>>> INFO Chain termini will be charged >>>>>>>> INFO Residues at chain brakes will not be charged >>>>>>>> INFO Local elastic bonds will be used for extended regions. >>>>>>>> INFO Position restraints will be generated. >>>>>>>> WARNING Position restraints are only enabled if -DPOSRES is set in >>>>>>>> the MDP file >>>>>>>> INFO Read input structure from file. >>>>>>>> INFO Input structure is a GRO file. Chains will be labeled >>>>>>>> consecutively. >>>>>>>> Traceback (most recent call last): >>>>>>>> File "./martinize-1.0.py", line 2306, in <module> >>>>>>>> for title,atoms,box in frameIterator(inStream): >>>>>>>> File "./martinize-1.0.py", line 1183, in groFrameIterator >>>>>>>> atoms = [groAtom(streamIterator.next()) for i in range(natoms)] >>>>>>>> File "./martinize-1.0.py", line 1170, in groAtom >>>>>>>> return (S(a[10:15]), S(a[5:10]), I(a[:5]), " ", >>>>>>>> 10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44])) >>>>>>>> ValueError: invalid literal for int() with base 10: '2.' >>>>>>>> >>>>>>>> I have used the command line ./martinize-1.0.py -f npt_strip_wat.gro >>>>>>>> -o frag_npt_cg_pdb.top -x frag_npt_cg_pdb.gro -v -p backbone >>>>>>>> >>>>>>>> were my input file is very simply >>>>>>>> >>>>>>>> Protein in water >>>>>>>> 2410 >>>>>>>> 1ALA N 1 1.497 1.862 1.290 0.1206 -0.3069 -0.2102 >>>>>>>> 1ALA H1 2 1.409 1.866 1.338 0.8590 -0.1748 1.1978 >>>>>>>> 1ALA H2 3 1.547 1.948 1.296 2.0372 -1.4201 0.8359 >>>>>>>> 1ALA H3 4 1.483 1.837 1.194 1.8924 -0.0993 -0.5621 >>>>>>>> 1ALA CA 5 1.585 1.753 1.335 -0.1231 -0.2165 0.4955 >>>>>>>> 1ALA CB 6 1.625 1.781 1.480 0.3554 -0.5405 0.4275 >>>>>>>> 1ALA C 7 1.517 1.617 1.323 0.1234 -0.2807 -0.1917 >>>>>>>> 1ALA O 8 1.407 1.624 1.268 -0.0033 0.4302 0.1378 >>>>>>>> 2GLU N 9 1.566 1.515 1.393 -0.2655 -0.2542 0.1191 >>>>>>>> 2GLU H 10 1.655 1.536 1.434 0.1561 0.1079 -0.9482 >>>>>>>> 2GLU CA 11 1.501 1.384 1.402 0.3096 -0.5394 0.1823 >>>>>>>> 2GLU CB 12 1.601 1.272 1.427 0.7527 -0.2033 -0.0775 >>>>>>>> 2GLU CG 13 1.694 1.280 1.548 -0.0279 0.1789 0.5017 >>>>>>>> 2GLU CD 14 1.779 1.405 1.571 0.4664 -0.1532 0.4921 >>>>>>>> 2GLU OE1 15 1.882 1.412 1.500 0.2904 -0.0189 0.2469 >>>>>>>> 2GLU OE2 16 1.740 1.489 1.654 0.2746 0.1001 0.1509 >>>>>>>> 2GLU C 17 1.378 1.355 1.489 0.5085 -0.1385 0.5964 >>>>>>>> 2GLU O 18 1.352 1.237 1.510 0.3837 -0.1792 0.2200 >>>>>>>> 3GLU N 19 1.307 1.458 1.535 -0.1887 -0.4392 0.2009 >>>>>>>> 3GLU H 20 1.315 1.547 1.489 -1.1961 0.1298 1.0835 >>>>>>>> 3GLU CA 21 1.180 1.436 1.604 -0.3118 -0.2722 0.0307 >>>>>>>> 3GLU CB 22 1.192 1.426 1.757 -0.3397 0.1329 0.0602 >>>>>>>> 3GLU C 23 1.066 1.533 1.572 -0.3117 -0.4554 -0.5274 >>>>>>>> 3GLU O1 24 1.072 1.606 1.471 0.0488 0.2651 0.0047 >>>>>>>> 3GLU O2 25 0.965 1.542 1.646 -0.1745 -0.2606 -0.3621 >>>>>>>> 2.91477 2.91477 2.91477 >>>>>>>> >>>>>>>> Can you help me on that? >>>>>>>> Thanks >>>>>>>> >>>>>>>> 2012/2/20 Tsjerk Wassenaar <tsje...@gmail.com>: >>>>>>>>> Hi Francesca, >>>>>>>>> >>>>>>>>> Is this the latest version >>>>>>>>> (http://md.chem.rug.nl/cgmartini/index.php/downloads/tools/204-martinize)? >>>>>>>>> If it is, please send me the input file and I'll fix the bug. Note >>>>>>>>> that the previous version that was available online was one used in a >>>>>>>>> workshop, while the script was still in beta. >>>>>>>>> >>>>>>>>> Cheers, >>>>>>>>> >>>>>>>>> Tsjerk >>>>>>>>> >>>>>>>>> >>>>>>>>> On Mon, Feb 20, 2012 at 10:43 AM, francesca vitalini >>>>>>>>> <francesca.vitalin...@gmail.com> wrote: >>>>>>>>>> Hi all, >>>>>>>>>> I'm trying to coarsegrain my structure using the script martinize.py >>>>>>>>>> and using my gro file as inmput and the dssp file with the second >>>>>>>>>> structure downloaded from http://swift.cmbi.ru.nl/gv/dssp using the >>>>>>>>>> pdb structure as input, I get the following error message that I >>>>>>>>>> really don't understand. >>>>>>>>>> >>>>>>>>>> INFO Chain termini will be charged >>>>>>>>>> INFO Residues at chain brakes will not be charged >>>>>>>>>> INFO Local elastic bonds will be used for extended regions. >>>>>>>>>> INFO Position restraints will be generated. >>>>>>>>>> WARNING Position restraints are only enabled if -DPOSRES is set in >>>>>>>>>> the MDP file >>>>>>>>>> INFO Read input structure from file. >>>>>>>>>> INFO Input structure is a GRO file. Chains will be labeled >>>>>>>>>> consecutively. >>>>>>>>>> Traceback (most recent call last): >>>>>>>>>> File "./martinize.py", line 2037, in <module> >>>>>>>>>> for title,atoms,box in frameIterator(inStream): >>>>>>>>>> File "./martinize.py", line 1303, in groFrameIterator >>>>>>>>>> atoms = [groAtom(streamIterator.next()) for i in range(natoms)] >>>>>>>>>> File "./martinize.py", line 1290, in groAtom >>>>>>>>>> return (S(a[10:15]), S(a[5:10]), I(a[:5]), " ", >>>>>>>>>> 10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44])) >>>>>>>>>> ValueError: invalid literal for int() with base 10: '2.' >>>>>>>>>> >>>>>>>>>> Can anyone help me on that? >>>>>>>>>> Thanks >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Francesca >>>>>>>>>> -- >>>>>>>>>> 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/Support/Mailing_Lists/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/Support/Mailing_Lists >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Tsjerk A. Wassenaar, Ph.D. >>>>>>>>> >>>>>>>>> post-doctoral researcher >>>>>>>>> Molecular Dynamics Group >>>>>>>>> * Groningen Institute for Biomolecular Research and Biotechnology >>>>>>>>> * Zernike Institute for Advanced Materials >>>>>>>>> University of Groningen >>>>>>>>> The Netherlands >>>>>>>>> -- >>>>>>>>> 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/Support/Mailing_Lists/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/Support/Mailing_Lists >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Francesca Vitalini >>>>>>>> >>>>>>>> PhD student at Computational Molecular Biology Group, >>>>>>>> Department of Mathematics and Informatics, FU-Berlin >>>>>>>> Arnimallee 6 14195 Berlin >>>>>>>> >>>>>>>> vital...@zedat.fu-berlin.de >>>>>>>> francesca.vital...@fu-berlin.de >>>>>>>> >>>>>>>> +49 3083875776 >>>>>>>> +49 3083875412 >>>>>>>> -- >>>>>>>> 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/Support/Mailing_Lists/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/Support/Mailing_Lists >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Tsjerk A. Wassenaar, Ph.D. >>>>>>> >>>>>>> post-doctoral researcher >>>>>>> Molecular Dynamics Group >>>>>>> * Groningen Institute for Biomolecular Research and Biotechnology >>>>>>> * Zernike Institute for Advanced Materials >>>>>>> University of Groningen >>>>>>> The Netherlands >>>>>>> -- >>>>>>> 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/Support/Mailing_Lists/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/Support/Mailing_Lists >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Francesca Vitalini >>>>>> >>>>>> PhD student at Computational Molecular Biology Group, >>>>>> Department of Mathematics and Informatics, FU-Berlin >>>>>> Arnimallee 6 14195 Berlin >>>>>> >>>>>> vital...@zedat.fu-berlin.de >>>>>> francesca.vital...@fu-berlin.de >>>>>> >>>>>> +49 3083875776 >>>>>> +49 3083875412 >>>>>> -- >>>>>> 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/Support/Mailing_Lists/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/Support/Mailing_Lists >>>>> >>>>> >>>>> >>>>> -- >>>>> Tsjerk A. Wassenaar, Ph.D. >>>>> >>>>> post-doctoral researcher >>>>> Molecular Dynamics Group >>>>> * Groningen Institute for Biomolecular Research and Biotechnology >>>>> * Zernike Institute for Advanced Materials >>>>> University of Groningen >>>>> The Netherlands >>>>> -- >>>>> 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/Support/Mailing_Lists/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/Support/Mailing_Lists >>>> >>>> >>>> >>>> -- >>>> Francesca Vitalini >>>> >>>> PhD student at Computational Molecular Biology Group, >>>> Department of Mathematics and Informatics, FU-Berlin >>>> Arnimallee 6 14195 Berlin >>>> >>>> vital...@zedat.fu-berlin.de >>>> francesca.vital...@fu-berlin.de >>>> >>>> +49 3083875776 >>>> +49 3083875412 >>>> -- >>>> 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/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >>> >>> >>> -- >>> Tsjerk A. Wassenaar, Ph.D. >>> >>> post-doctoral researcher >>> Molecular Dynamics Group >>> * Groningen Institute for Biomolecular Research and Biotechnology >>> * Zernike Institute for Advanced Materials >>> University of Groningen >>> The Netherlands >>> -- >>> 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/Support/Mailing_Lists/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/Support/Mailing_Lists >> >> >> >> -- >> Francesca Vitalini >> >> PhD student at Computational Molecular Biology Group, >> Department of Mathematics and Informatics, FU-Berlin >> Arnimallee 6 14195 Berlin >> >> vital...@zedat.fu-berlin.de >> francesca.vital...@fu-berlin.de >> >> +49 3083875776 >> +49 3083875412 > > > > -- > Francesca Vitalini > > PhD student at Computational Molecular Biology Group, > Department of Mathematics and Informatics, FU-Berlin > Arnimallee 6 14195 Berlin > > vital...@zedat.fu-berlin.de > francesca.vital...@fu-berlin.de > > +49 3083875776 > +49 3083875412 > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
