HI GROMACS users, Thank you mark for your advice.. As per these link http://en.wikipedia.org/wiki/Flying_ice_cube .... such as those using explicitly represented solvent under periodic boundary conditions - only the translational motion should be removed. Although it does not produce a perfectly continuous trajectory, periodic reassignment of velocities as in the Andersen thermostat method also minimize the problem......
So I have to use the comm_mode linear when explicit solvent is used, is it right?? If I used Nose - Hoover thermostat Is then comm_mode is needed to use..? (AS per your link ..More conservatively, the rate of velocity rescaling can be reduced, the scale factor computed over a time-averaged sample of instantaneous temperatures, or an alternative means of thermostatting such as the Nosé-Hoover thermostat can be used.) Thank you a lot in advance On Mon, Feb 20, 2012 at 7:20 PM, <gmx-users-requ...@gromacs.org> wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: problems with martinize.py (francesca vitalini) > 2. Re: Molecular Dynamics basics... (Mark Abraham) > 3. Re: problems with martinize.py (Tsjerk Wassenaar) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 20 Feb 2012 14:34:45 +0100 > From: francesca vitalini <francesca.vitalin...@gmail.com> > Subject: Re: [gmx-users] problems with martinize.py > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <caprcf+k1x4qy20azmicvzkeibncl3kai-0x147vpprr+aga...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > 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 > > > ------------------------------ > > Message: 2 > Date: Tue, 21 Feb 2012 00:41:27 +1100 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] Molecular Dynamics basics... > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4f424d87.1080...@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 21/02/2012 12:11 AM, prashant kurkute wrote: >> Hi GROMACS users, >> I am a very novice to GROMACS.. .. >> My question may be very simple but very important to me..!!! >> These may be very basics... >> >> 1. What is the meaning of comm_mode and nstcomm.. >> I read the manual but unable to digest it..so please >> explain in more detail along with its effect on system.. > > http://en.wikipedia.org/wiki/Flying_ice_cube > >> >> 2. When I am want to study self assembly of protein what >> should my comm_mode -linear or angular or none ?? > > You choose based on the above. > >> >> 3. what is the meaning of emtol in minimisation proces?? >> Should I take emtol value more or less to come to minimum energy >> state ??? > > What's not clear in manual section 7.3.5? > >> the structure on which I am working is not having any >> crystal or NMR structure , so I need the maximum energy >> minimised structure >> >> 4. When I am doing energy minimisation the gromacs shows >> (potential energy= -2.07) >> conjugate gradient step wise to small or no change in energy . >> converged to machine precision in 15881 step >> but dindn´t reach to the requested Fmax<10 > > You are minimizing a noisy function (cutoffs), so oscillation or > apparent stagnation near a stationary point can occur. See manual 3.10 > >> What should to do?? >> or the structure I get is energy minimised or not..??? > > That depends what you want to do with it next. For MD, it's probably fine. > > Mark > > > ------------------------------ > > Message: 3 > Date: Mon, 20 Feb 2012 14:49:35 +0100 > From: Tsjerk Wassenaar <tsje...@gmail.com> > Subject: Re: [gmx-users] problems with martinize.py > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <cabze1sirhe1fklvnfnannirbuachc2lhqz2_d7kp-nda6sa...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > 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! > > End of gmx-users Digest, Vol 94, Issue 119 > ****************************************** -- 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