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 /<[EMAIL PROTECTED]>/ schrieb am *Mo, 7.7.2008:
*
*Von: Justin A. Lemkul <[EMAIL PROTECTED]>
Betreff: Re: [gmx-users] lipid itp problem
An: [EMAIL PROTECTED], "Gromacs Users' List" <[email protected]>
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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