<table cellspacing='0' cellpadding='0' border='0' ><tr><td valign='top' style='font: inherit;'><P>Thanks Tsjerk,</P>
<P> </P>
<P>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.</P>
<P> </P>
<P> </P>
<P>Serdar</P>
<P> </P>
<P><BR><BR>--- Tsjerk Wassenaar <I><tsjerkw@gmail.com></I></B> schrieb am <B>Mi, 9.7.2008:<BR></P>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid">Von: Tsjerk Wassenaar <tsjerkw@gmail.com><BR>Betreff: Re: [gmx-users] lipid itp file problem<BR>An: "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>Datum: Mittwoch, 9. Juli 2008, 8:29<BR><BR><PRE>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@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@vt.edu>/ schrieb am *Mo,
7.7.2008:
>> *
>>
>> *Von: Justin A. Lemkul <jalemkul@vt.edu>
>> Betreff: Re: [gmx-users] lipid itp problem
>> An: durdagis@yahoo.de, "Gromacs Users' List"
<gmx-users@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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