[gmx-users] lipid itp file problem

Wed Jul 9 10:21:45 CEST 2008

Hi Serdar,

Well, now you're in for it! Up to you to see if you can reproduce the
experimental area per lipid, phase transitions and what else there is
in lipid parameterization targets. Don't you dare to do simulations of
a protein-lipid system before you have proven you've got these right.

Good luck!

Tsjerk

On Wed, Jul 9, 2008 at 9:46 AM, serdar durdagi <durdagis at yahoo.de> wrote:
> Thanks Tsjerk,
>
>
>
> Actually I solved the problem. Previously, I was using coordinates from
> output of simulation by AMBER for DPPC molecules and try to get ff from
> PRODRG. Now, I used DPPC pdb file from Tieleman's web site and I produced
> Gromos96 ff from PRODRG again. At the begining, it seems bond lengths
> between phosphate and oxygens are very long but during the minimization they
> come to expected values.
>
>
>
>
>
> Serdar
>
>
>
> --- Tsjerk Wassenaar <tsjerkw at gmail.com> schrieb am Mi, 9.7.2008:
>
> Von: Tsjerk Wassenaar <tsjerkw at gmail.com>
> Betreff: Re: [gmx-users] lipid itp file problem
> An: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Datum: Mittwoch, 9. Juli 2008, 8:29
>
> Hi,
>
> Besides, there are parameters around for DPPC for the newer GROMOS96
> force fields. PRODRG is unlikely to yield better results. Better check
> literature (Marrink's group, Tieleman's group). That is, unless
> there's a specific reason to use PRODRG, e.g. comparing results with
> standard parameterization.
>
> Cheers,
>
> Tsjerk
>
> On Mon, Jul 7, 2008 at 6:55 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> It's difficult to tell what's going on.  You're using
> non-standard
>> nomeclature for your atoms, so it's hard to tell where you got that
>> structure file.  Typically, one sees DPPC start with C1, C2, C3, N4, etc.
>> running sequentially with the normal numbering.
>> Be aware that PRODRG is not changing atom *types* since this information
> is
>> not in a coordinate file.  PRODRG has its own way of numbering and writing
>> its output, so it is not terribly surprising that there are some
>> differences.
>>
>> It looks like there is something screwy with the input.pdb, though.  The
>> oxygen atoms at the phosphate moiety show up disconnected in VMD, so the
>> bonds are probably too long, and perhaps something is problematic there.
>>  When I run your coordinates through PRODRG (to replicate the problem),
>> PRODRG doesn't even generate a whole molecule, it finds two fragments!
>  So I
>> don't know how you even succeeded in getting this output .gro file.
>>
>> I'm assuming you already have a bilayer system from some source, since
> you
>> had previously implanted a protein and whatever else.  Draw the molecule
> in
>> PRODRG with the JME editor and see if it successfully runs.  The atom
>> nomenclature will be very different from standard numbering, but at least
> it
>> will produce a complete topology.  Adjust the atom names to what they
> should
>> be and try minimizing your structure again.
>>
>> -Justin
>>
>>
>> serdar durdagi wrote:
>>>
>>> Dear all,
>>>
>>>
>>> I used beta version of PRODRG to produce G43a1 ff for a single DPPC
>>> molecule. When I try to make geometry optimisation, always I am facing
> with
>>> large Fmax values and large 1-4 interaction value.
>>>
>>>
>>> When I visualize the *.gro file of the output, it seems some atom
> types
>>> are changed!
>>>
>>>
>>> I am attaching input pdb file and output gro file.
>>>
>>>
>>> What is the wrong thing here? Could any body tell me please?
>>>
>>>
>>>
>>> Serdar
>>>
>>>
>>> input pdb file:
>>>
>>>
>>> TITLE Gyas ROwers Mature At Cryogenic Speed
>>>
>>> REMARK THIS IS A SIMULATION BOX
>>>
>>> CRYST1 45.149 45.149 45.149 90.00 90.00 90.00 P 1 1
>>>
>>> MODEL 1
>>>
>>> HETATM 1 N1 MOL 1 34.444 18.233 25.460 1.00 0.00
>>>
>>> HETATM 2 C7 MOL 1 35.570 19.239 25.501 1.00 0.00
>>>
>>> HETATM 3 C6 MOL 1 35.017 16.871 25.137 1.00 0.00
>>>
>>> HETATM 4 C5 MOL 1 33.796 18.184 26.832 1.00 0.00
>>>
>>> HETATM 5 C2 MOL 1 33.479 18.667 24.357 1.00 0.00
>>>
>>> HETATM 6 C3 MOL 1 32.028 18.158 24.509 1.00 0.00
>>>
>>> HETATM 7 O4 MOL 1 31.392 18.891 25.581 1.00 0.00
>>>
>>> HETATM 8 P8 MOL 1 29.882 18.565 25.912 1.00 0.00
>>>
>>> HETATM 9 O9 MOL 1 29.334 17.523 25.021 1.00 0.00
>>>
>>> HETATM 10 O11 MOL 1 29.292 19.999 25.571 1.00 0.00
>>>
>>> HETATM 11 C12 MOL 1 28.661 20.699 26.667 1.00 0.00
>>>
>>> HETATM 12 C13 MOL 1 27.887 21.958 26.219 1.00 0.00
>>>
>>> HETATM 13 O31 MOL 1 26.485 21.650 25.948 1.00 0.00
>>>
>>> HETATM 14 C32 MOL 1 26.067 20.880 24.918 1.00 0.00
>>>
>>> HETATM 15 O46 MOL 1 26.794 20.369 24.088 1.00 0.00
>>>
>>> HETATM 16 C33 MOL 1 24.556 20.779 24.890 1.00 0.00
>>>
>>> HETATM 17 C34 MOL 1 23.968 21.111 23.497 1.00 0.00
>>>
>>> HETATM 18 C35 MOL 1 22.446 21.361 23.564 1.00 0.00
>>>
>>> HETATM 19 C36 MOL 1 21.866 21.656 22.162 1.00 0.00
>>>
>>> HETATM 20 C37 MOL 1 20.364 22.006 22.249 1.00 0.00
>>>
>>> HETATM 21 C38 MOL 1 19.701 22.059 20.856 1.00 0.00
>>>
>>> HETATM 22 C39 MOL 1 18.202 22.412 20.975 1.00 0.00
>>>
>>> HETATM 23 C40 MOL 1 17.447 22.130 19.660 1.00 0.00
>>>
>>> HETATM 24 C41 MOL 1 15.956 22.512 19.778 1.00 0.00
>>>
>>> HETATM 25 C42 MOL 1 15.163 22.060 18.534 1.00 0.00
>>>
>>> HETATM 26 C43 MOL 1 13.677 22.462 18.642 1.00 0.00
>>>
>>> HETATM 27 C44 MOL 1 12.876 21.978 17.413 1.00 0.00
>>>
>>> HETATM 28 C45 MOL 1 11.392 22.382 17.522 1.00 0.00
>>>
>>> HETATM 29 C1 MOL 1 10.593 21.928 16.284 1.00 0.00
>>>
>>> HETATM 30 C8 MOL 1 9.112 22.333 16.402 1.00 0.00
>>>
>>> HETATM 31 C14 MOL 1 28.585 22.745 25.083 1.00 0.00
>>>
>>> HETATM 32 O15 MOL 1 28.067 24.102 25.033 1.00 0.00
>>>
>>> HETATM 33 C16 MOL 1 26.879 24.330 24.441 1.00 0.00
>>>
>>> HETATM 34 O30 MOL 1 26.330 23.544 23.703 1.00 0.00
>>>
>>> HETATM 35 C17 MOL 1 26.294 25.661 24.826 1.00 0.00
>>>
>>> HETATM 36 C18 MOL 1 24.751 25.657 24.891 1.00 0.00
>>>
>>> HETATM 37 C19 MOL 1 24.067 25.811 23.515 1.00 0.00
>>>
>>> HETATM 38 C20 MOL 1 22.542 25.943 23.704 1.00 0.00
>>>
>>> HETATM 39 C21 MOL 1 21.791 26.100 22.367 1.00 0.00
>>>
>>> HETATM 40 C22 MOL 1 20.287 26.328 22.625 1.00 0.00
>>>
>>> HETATM 41 C23 MOL 1 19.486 26.449 21.314 1.00 0.00
>>>
>>> HETATM 42 C24 MOL 1 17.984 26.636 21.604 1.00 0.00
>>>
>>> HETATM 43 C25 MOL 1 17.163 26.715 20.301 1.00 0.00
>>>
>>> HETATM 44 C26 MOL 1 15.652 26.784 20.601 1.00 0.00
>>>
>>> HETATM 45 C27 MOL 1 14.825 26.856 19.302 1.00 0.00
>>>
>>> HETATM 46 C28 MOL 1 13.315 26.838 19.610 1.00 0.00
>>>
>>> HETATM 47 C29 MOL 1 12.478 26.954 18.320 1.00 0.00
>>>
>>> HETATM 48 C9 MOL 1 10.969 26.915 18.635 1.00 0.00
>>>
>>> HETATM 49 C10 MOL 1 10.129 27.155 17.369 1.00 0.00
>>>
>>> HETATM 50 O10 MOL 1 29.702 18.159 27.328 1.00 0.00
>>>
>>> TER
>>>
>>> ENDMDL
>>>
>>>
>>>
>>> output pdb file
>>>
>>>
>>>
>>> GROningen MAchine for Chemical Simulation in water
>>>
>>> 50
>>>
>>> 1MOL C31 1 3.445 1.823 2.546
>>>
>>> 1MOL C30 2 3.557 1.924 2.550
>>>
>>> 1MOL C29 3 3.502 1.687 2.514
>>>
>>> 1MOL C28 4 3.379 1.818 2.683
>>>
>>> 1MOL C27 5 3.347 1.867 2.435
>>>
>>> 1MOL C26 6 3.203 1.816 2.451
>>>
>>> 1MOL C25 7 3.139 1.889 2.558
>>>
>>> 1MOL C24 8 2.988 1.856 2.591
>>>
>>> 1MOL C23 9 2.933 1.752 2.502
>>>
>>> 1MOL C22 10 2.929 2.000 2.557
>>>
>>> 1MOL C21 11 2.866 2.070 2.667
>>>
>>> 1MOL C20 12 2.788 2.195 2.622
>>>
>>> 1MOL C19 13 2.648 2.165 2.595
>>>
>>> 1MOL C18 14 2.607 2.088 2.492
>>>
>>> 1MOL C17 15 2.679 2.037 2.409
>>>
>>> 1MOL C15 16 2.456 2.078 2.489
>>>
>>> 1MOL O16 17 2.397 2.111 2.350
>>>
>>> 1MOL O14 18 2.245 2.136 2.356
>>>
>>> 1MOL C13 19 2.187 2.166 2.216
>>>
>>> 1MOL C12 20 2.036 2.201 2.225
>>>
>>> 1MOL O11 21 1.970 2.206 2.086
>>>
>>> 1MOL P8 22 1.820 2.241 2.097
>>>
>>> 1MOL O9 23 1.745 2.213 1.966
>>>
>>> 1MOL O10 24 1.596 2.251 1.978
>>>
>>> 1MOL O7 25 1.516 2.206 1.853
>>>
>>> 1MOL C6 26 1.368 2.246 1.864
>>>
>>> 1MOL C5 27 1.288 2.198 1.741
>>>
>>> 1MOL N4 28 1.139 2.238 1.752
>>>
>>> 1MOL C2 29 1.059 2.193 1.628
>>>
>>> 1MOL C3 30 0.911 2.233 1.640
>>>
>>> 1MOL C1 31 2.859 2.273 2.508
>>>
>>> 1MOL C32 32 2.806 2.412 2.503
>>>
>>> 1MOL O33 33 2.688 2.433 2.444
>>>
>>> 1MOL C34 34 2.633 2.354 2.370
>>>
>>> 1MOL O35 35 2.629 2.566 2.483
>>>
>>> 1MOL C36 36 2.475 2.566 2.489
>>>
>>> 1MOL C37 37 2.407 2.581 2.352
>>>
>>> 1MOL C38 38 2.254 2.594 2.370
>>>
>>> 1MOL C39 39 2.179 2.610 2.237
>>>
>>> 1MOL C40 40 2.029 2.633 2.262
>>>
>>> 1MOL C41 41 1.949 2.645 2.131
>>>
>>> 1MOL C42 42 1.798 2.664 2.160
>>>
>>> 1MOL C43 43 1.716 2.671 2.030
>>>
>>> 1MOL C44 44 1.565 2.678 2.060
>>>
>>> 1MOL C45 45 1.482 2.686 1.930
>>>
>>> 1MOL C46 46 1.332 2.684 1.961
>>>
>>> 1MOL C47 47 1.248 2.695 1.832
>>>
>>> 1MOL C48 48 1.097 2.692 1.864
>>>
>>> 1MOL C49 49 1.013 2.715 1.737
>>>
>>> 1MOL C50 50 2.970 1.816 2.733
>>>
>>> 4.51490 4.51490 4.51490
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> --- Justin A. Lemkul /<jalemkul at vt.edu>/ schrieb am *Mo,
> 7.7.2008:
>>> *
>>>
>>>    *Von: Justin A. Lemkul <jalemkul at vt.edu>
>>>    Betreff: Re: [gmx-users] lipid itp problem
>>>    An: durdagis at yahoo.de, "Gromacs Users' List"
> <gmx-users at gromacs.org>
>>>    Datum: Montag, 7. Juli 2008, 14:06
>>>
>>>    *
>>>
>>>    *Please make sure to include the gmx-users list on correspondence;
>>>  someone else may have a useful idea.
>>>
>>>    It looks to me that your "input.pdb" is badly broken.  Is
> this what
>>>  PRODRG generated?  Are you using this structure for anything?  Where
> are
>>>  the coordinates for your lipid bilayer coming from?
>>>
>>>    I would suggest starting over with the minimization - take the .pdb
>>> file    that PRODRG generates (united-atom representation, as
> you've tried
>>> to    use here), center it in a large box to avoid PBC effects (using
>>> editconf    -c), and try again.
>>>
>>>    Just a general thought as well - it has long been said over this
> list
>>>  that ffgmx should not be used for any new production simulations.  It
> is
>>>  deprecated and the results from it may not be as reliable as one of
> the
>>>  newer, Gromos96 force fields.  I would suggest using the PRODRG beta
>>>  server to generate parameters under Gromos96 43a1.  None of this is
>>>  likely the root cause of your problem, however.
>>>
>>>    -Justin========================================*
>>>
>>>
>>>
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>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>>
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>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> _______________________________________________
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>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623