[gmx-users] Re: gmx-users Digest, Vol 94, Issue 119
prashant kurkute
prashantkurkute2 at gmail.com
Mon Feb 20 16:22:57 CET 2012
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-request at gromacs.org> wrote:
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> 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.vitalini11 at gmail.com>
> Subject: Re: [gmx-users] problems with martinize.py
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CAPRCF+K1x4Qy20AzmicvZKeibnCL3kai-0X147vpPRr+agA-9g at 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 <tsjerkw at 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.vitalini11 at 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 <tsjerkw at 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.vitalini11 at 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 <tsjerkw at 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.vitalini11 at 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 at 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-request at 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 at 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-request at 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
>>>>>
>>>>> vitalini at zedat.fu-berlin.de
>>>>> francesca.vitalini at fu-berlin.de
>>>>>
>>>>> +49 3083875776
>>>>> +49 3083875412
>>>>> --
>>>>> gmx-users mailing list gmx-users at 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-request at 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 at 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-request at 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
>>>
>>> vitalini at zedat.fu-berlin.de
>>> francesca.vitalini at fu-berlin.de
>>>
>>> +49 3083875776
>>> +49 3083875412
>>> --
>>> gmx-users mailing list gmx-users at 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-request at 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 at 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-request at 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
>
> vitalini at zedat.fu-berlin.de
> francesca.vitalini at fu-berlin.de
>
> +49 3083875776
> +49 3083875412
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 21 Feb 2012 00:41:27 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Molecular Dynamics basics...
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F424D87.1080605 at 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 <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] problems with martinize.py
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CABzE1SiRhe1fkLvnFnANniRBUachC2LHqz2_d7kP-Nda6sakEQ at 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.vitalini11 at 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 <tsjerkw at 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.vitalini11 at 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 <tsjerkw at 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.vitalini11 at 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 <tsjerkw at 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.vitalini11 at 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 at 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!
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>>>>>>>> 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 at 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!
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>>>>>>> www interface or send it to gmx-users-request at 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
>>>>>>
>>>>>> vitalini at zedat.fu-berlin.de
>>>>>> francesca.vitalini at fu-berlin.de
>>>>>>
>>>>>> +49 3083875776
>>>>>> +49 3083875412
>>>>>> --
>>>>>> gmx-users mailing list gmx-users at 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-request at 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 at 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!
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>>>>> www interface or send it to gmx-users-request at 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
>>>>
>>>> vitalini at zedat.fu-berlin.de
>>>> francesca.vitalini at fu-berlin.de
>>>>
>>>> +49 3083875776
>>>> +49 3083875412
>>>> --
>>>> gmx-users mailing list gmx-users at 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!
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>>>> www interface or send it to gmx-users-request at 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 at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>> www interface or send it to gmx-users-request at 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
>>
>> vitalini at zedat.fu-berlin.de
>> francesca.vitalini at fu-berlin.de
>>
>> +49 3083875776
>> +49 3083875412
>> --
>> gmx-users mailing list gmx-users at 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-request at 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 at 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
> ******************************************
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