[gmx-users] Nubmer of coordinate not matching in topol.top and sol.gro
Sangita Kachhap
sangita at imtech.res.in
Thu May 3 07:10:00 CEST 2012
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> Today's Topics:
>
> 1. Re: doubt about OpenMM (Martin Hoefling)
> 2. Re: doubt about OpenMM (Thales Kronenberger)
> 3. pullf.xvg (Krzysztof Kuczera)
> 4. Pull code for Constraint (xu zhijun)
> 5. Re: Number of cooredinate in topol.top and solv.gro not
> matching (Justin A. Lemkul)
> 6. RE: pullf.xvg (Marzinek, Jan)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 02 May 2012 19:31:02 +0200
> From: Martin Hoefling <martin.hoefling at googlemail.com>
> Subject: Re: [gmx-users] doubt about OpenMM
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4FA16F56.1010701 at googlemail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Am 30.04.2012 19:32, schrieb Thales Kronenberger:
>
> Hey Folks,
>
>> SUDO_USER=laboratorio24
>> PWD=/home/laboratorio24/OpenMM4.0-Linux64/python
>> File "setup.py", line 165
>> print "%s" % outputString
>> ^
>> SyntaxError: invalid syntax
>> INSTALLATION FAILED
>
> which python version are you using? For versions >= 3.0, the above
> syntax is not allowed anymore, afair.
>
> Best
>
> Martin
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 2 May 2012 14:32:59 -0300
> From: Thales Kronenberger <kronenberger7 at gmail.com>
> Subject: Re: [gmx-users] doubt about OpenMM
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CA+S5A5ot0cay=1tJu-_iE9Je+roQWP5fz=Xk3T8=VuBqvU+xhQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I have Python 2.6.5
>
> 2012/5/2 Martin Hoefling <martin.hoefling at googlemail.com>
>
>> Am 30.04.2012 19:32, schrieb Thales Kronenberger:
>>
>> Hey Folks,
>>
>> > SUDO_USER=laboratorio24
>> > PWD=/home/laboratorio24/OpenMM4.0-Linux64/python
>> > File "setup.py", line 165
>> > print "%s" % outputString
>> > ^
>> > SyntaxError: invalid syntax
>> > INSTALLATION FAILED
>>
>> which python version are you using? For versions >= 3.0, the above
>> syntax is not allowed anymore, afair.
>>
>> Best
>>
>> Martin
>> --
>> gmx-users mailing list gmx-users at gromacs.org
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> ------------------------------
>
> Message: 3
> Date: Wed, 2 May 2012 12:38:29 -0500
> From: Krzysztof Kuczera <kkuczera at ku.edu>
> Subject: [gmx-users] pullf.xvg
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4FA17115.6000806 at ku.edu>
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>
> Could someone please tell me what exactly is printed in the pullf.xvg
> file from an umbrella sampling simulation?
> Is it the total force acting the COM of the pull group - i.e. force from
> regular potential plus the umbrella force or just the unbiased force?
>
> Krzysztof Kuczera
>
> --
> Krzysztof Kuczera
> Departments of Chemistry and Molecular Biosciences
> The University of Kansas
> 2010 Malott Hall
> Lawrence, KS 66045
> Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu
> http://oolung.chem.ku.edu/~kuczera/home.html
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 2 May 2012 10:40:25 -0700 (PDT)
> From: xu zhijun <simulationxu at yahoo.com>
> Subject: [gmx-users] Pull code for Constraint
> To: gmx-users at gromacs.org
> Message-ID:
> <1335980425.78289.YahooMailClassic at web162001.mail.bf1.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I try to pull the small molecule from the bulk solution to the surface by the
> Constraint function.
> However, it seems that it does not work well.
>
> Here my part of run parameters about the Constraint in my mdp file
>
> ##############################
>
> constraints???? = all-bonds; hbonds; all-bonds
> constraint-algorithm???? = Lincs
>
> pull??????????? = constraint
> pull_geometry?? = distance
> pull_dim??????? = N N Y
> pull_ngroups??? = 1
> pull_group0???? = Surface
> pull_group1???? = Protein
> pull_nstxout??? = 1000
> pull_nstfout??? = 1000
> pull_rate1????? = -0.001
> pull_init1????? = 1.73331
> ##########################
>
> Based my understanding, the pull_rate1 is about -0.001/ps.
> That means in the pullx.xvg file, the distance shoud be as follows (only the
> z-distance shown, time step is 1fs.)
> 1.73331
> 1.72231
> 1.72131
> 1.72031
> .
> .
> However, in my simulation, the results from the simulation is as follow:
> 1.73331
> 1.71154
> 1.75043
> 1.73213
> 1.78065
> 1.79769
> 1.84298
> 1.87008
>
> It seems some force has been imposed on the pull molecules.
> But in the pullf.xvg the force is ZERO.
> I used the latest gromacs version, But for the gromacs4.0 it works very well
> (works as what I think).
> Can someone help me about the issue?
>
> Thanks a lot
>
> Jerry
>
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> ------------------------------
>
> Message: 5
> Date: Wed, 02 May 2012 13:43:18 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Number of cooredinate in topol.top and
> solv.gro not matching
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4FA17236.3040807 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
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>
>
> On 5/2/12 1:09 PM, Sangita Kachhap wrote:
>
>>>> I have to do MD simulation of ligand bound membrane protein in lipid
>>>> bilayer.
>>>> Thus I am doing tutorialfor Protein - Ligand tutorial:
>>>>
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
>>>>
>>>> I have used following command:
>>>>
>>>> pdb2gmx -f 3HTB_clean.pdb -o conf.gro -water spc
>>>>
>>>> editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0
>>>>
>>>> genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
>>>>
>>>> grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
>>>>
>>>> I am getting stuck at last command. Its showing following error:
>>>>
>>>> Fatal error:
>>>> number of coordinates in coordinate file (solv.gro, 33049)
>>>> does not match topology (topol.top, 33064)
>>>> For more information and tips for troubleshooting, please check the GROMACS
>>>> website at http://www.gromacs.org/Documentation/Errors
>>>>
>>>
>>> Did you follow the link? Did you read
>>> http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
>>> ?
>>>
>>>> {But when I calculate number of atom in topol.top and solv.gro it is same}
>>>>
>>>
>>> That's not possible.
>>>
>>>> When I checked above http: I got that such type of error may be due to cpp
>>>> variable is not properly set in the .mdp file.
>>>> But When I locate ccp in my system and add it to .mdp file.
>>>>
>>>> "
>>>> ; LINES STARTING WITH ';' ARE COMMENTS
>>>> title = Minimization ; Title of run
>>>> cpp =/usr/bin/cpp
>>>> ; Parameters describing what to do, when to stop and what to save
>>>> "
>>>>
>>>> Then also it showing same error.
>>>>
>>>> Please help me to solve this problem.
>>>>
>>>> I am using gromacs-4.5.5 and installed with fftw-3.3.1 .
>>>>
>>>
>>> The cpp parameter is ignored for all Gromacs versions as of 4.5.
>>>
>>> Your problem is that you don't have a ligand in your coordinate file. Note
>>> that
>>> you're off by 15 atoms, which is exactly how many are in the ligand described
>>> in
>>> the tutorial. Go back and read the instructions closely, as appending the
>>> ligand to the protein coordinate file is discussed in detail.
>>
>>
>>
>> Thanks for reply
>>
>> When I am appending ligand from .gro file and generating complex the new .gro
>> file newbox.gro do not have ligand.
>>
>> Command I have used: editconf -f conf.gro -o newbox.gro -bt dodecahedron -d
>> 1.0
>>
>> I am appending ligand like this at the end of conf.gro
>>
>> 163ASN HD21 1689 1.029 -0.671 -0.401
>> 163ASN HD22 1690 0.944 -0.584 -0.525
>> 163ASN C 1691 0.621 -0.740 -0.126
>> 163ASN O1 1692 0.624 -0.616 -0.140
>> 163ASN O2 1693 0.683 -0.703 -0.011
>> 1JZ4 C4 1 2.429 -2.412 -0.007
>> 1JZ4 C14 2 2.392 -2.470 -0.139
>> 1JZ4 C13 3 2.246 -2.441 -0.181
>> 1JZ4 C12 4 2.229 -2.519 -0.308
>> 1JZ4 C11 5 2.169 -2.646 -0.295
>> 1JZ4 H11 6 2.135 -2.683 -0.199
>> 1JZ4 C7 7 2.155 -2.721 -0.411
>> 1JZ4 H7 8 2.104 -2.817 -0.407
>> 1JZ4 C8 9 2.207 -2.675 -0.533
>> 1JZ4 H8 10 2.199 -2.738 -0.621
>> 1JZ4 C9 11 2.267 -2.551 -0.545
>> 1JZ4 H9 12 2.306 -2.516 -0.640
>> 1JZ4 C10 13 2.277 -2.473 -0.430
>> 1JZ4 OAB 14 2.341 -2.354 -0.434
>> 1JZ4 HAB 15 2.369 -2.334 -0.528
>> 5.99500 5.19182 9.66100 0.00000 0.00000 -2.99750 0.00000
>> 0.00000
>> 0.00000
>>
>
> Have you correctly incremented the second line of conf.gro to indicate that more
> atoms have been added? Without it, editconf will read the wrong number of lines
> and exclude the ligand.
>
Thanks for reply.
I have changed line number in conf.gro and now its working.
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 2 May 2012 19:08:08 +0000
> From: "Marzinek, Jan" <j.marzinek10 at imperial.ac.uk>
> Subject: RE: [gmx-users] pullf.xvg
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <787E9EFEEFC7384580812E4CA26D4F4409FE6762 at icexch-m4.ic.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
>
>
>
>
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of
> Krzysztof Kuczera [kkuczera at ku.edu]
> Sent: Wednesday, May 02, 2012 6:38 PM
> To: Discussion list for GROMACS users
> Subject: [gmx-users] pullf.xvg
>
> Could someone please tell me what exactly is printed in the pullf.xvg
> file from an umbrella sampling simulation?
> Is it the total force acting the COM of the pull group - i.e. force from
> regular potential plus the umbrella force or just the unbiased force?
>
> Krzysztof Kuczera
>
>
>
> Each window in umbrella sampling simulation gives you the biased potential which
> is the harmonic potential. The wham allows you to combine all windows by
> applying weights and calculating the unbiased potential which requires
> calculation of the free enerrgy associated with introducing the harmonic pontial
> (biased). Please, search literature to see equations.
>
> Jan
>
> --
> Krzysztof Kuczera
> Departments of Chemistry and Molecular Biosciences
> The University of Kansas
> 2010 Malott Hall
> Lawrence, KS 66045
> Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu
> http://oolung.chem.ku.edu/~kuczera/home.html
>
>
>
> --
> 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
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> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> ------------------------------
>
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> End of gmx-users Digest, Vol 97, Issue 18
> *****************************************
>
With regards
Sangita Kachhap
SRF
BIC,IMTECH
CHANDIGARH
______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
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