[gmx-users] Re: atom types, residue info for D-amino acids
Daan van Aalten
vdava at davapc1.bioch.dundee.ac.uk
Sat May 31 10:24:00 CEST 2003
Regina
I'm afraid you are missing the point! You are confusing atom NAMES
with atom TYPES, and you are thinking GROMACS won't treat your
peptide properly, simply because PRODRG doesn't call the residues PHE PRO
etc. FORGET for a moment that your peptide is a peptide, but think of it
as a molecule with a random collection of atoms, with random names, with
the residue name UNK. You put this into PRODRG. Despite the random names,
PRODRG recognizes that the CHEMISTRY of these atoms can be captured by
assigning atom TYPES (which you can *NOT* see in the PDB file), bonds,
angles etc. as part of a TOPOLOGY file.
If you don;t understand this, it's really time to RTFM as they say on the
CCP4 mailing list!
cheers
Daan
On Fri, 30 May 2003, Regina R. Monaco, Ph.D. wrote:
> HI Daan-
>
> Thanks for your interest with my problem. I can get a working output
> .pdb file from PRODRG2, and run it through GROMACS. The simulation will
> run. The problem is that it looks as if the atom types are incorrect,
> and none of the residues are labeled as such (ie, the entire molecule,
> which is a hexapeptide, is considered in the .pdb file as a single
> residue designated as "DRG", instead of each residue being identified
> as belonging to a "PRO" (i.e., proline), "PHE" or whichever residue it
> actually is. I am most concerned about the atom types, and also about
> being able to identify which atoms belong to which residues by looking
> at the .pdb file itself (for editing and other purposes).
>
> Heres the output PRODRG2 gave me as a pdb for my molecule:
>
> REMARK
> REMARK
> REMARK This file was generated by PRODRG version 030513.0284
> REMARK PRODRG written/copyrighted by Daan van Aalten
> REMARK
> REMARK Questions/comments to dava at davapc1.bioch.dundee.ac.uk
> REMARK
> REMARK When using this software in a publication, cite:
> REMARK D.M.F. van Aalten, R. Bywater, J.B.C. Findlay,
> REMARK M. Hendlich, R.W.W. Hooft and G. Vriend,
> REMARK PRODRG, a program for generating molecular topologies
> REMARK and unique molecular descriptors from coordinates
> REMARK of small molecules.
> REMARK Journal of Computer Aided Molecular Design (1996), 10, 255-262.
> REMARK
> REMARK
> HETATM 1 N2 DRG 1 3.190 -11.050 -14.770 1.00 20.00
> N
> HETATM 2 C5 DRG 1 1.840 -11.620 -14.710 1.00 20.00
> C
> HETATM 3 C4 DRG 1 1.890 -13.080 -14.260 1.00 20.00
> C
> HETATM 4 C3 DRG 1 0.460 -13.600 -14.170 1.00 20.00
> C
> HETATM 5 C2 DRG 1 0.330 -15.060 -13.690 1.00 20.00
> C
> HETATM 6 C1 DRG 1 -1.130 -15.510 -13.450 1.00 20.00
> C
> HETATM 7 N1 DRG 1 -1.690 -15.010 -12.180 1.00 20.00
> N
> HETATM 8 C6 DRG 1 -2.140 -15.280 -14.590 1.00 20.00
> C
> HETATM 9 O1 DRG 1 -3.330 -15.280 -14.280 1.00 20.00
> O
> HETATM 10 N3 DRG 1 -1.710 -15.100 -15.840 1.00 20.00
> N
> HETATM 11 C7 DRG 1 -2.580 -14.610 -16.930 1.00 20.00
> C
> HETATM 12 C8 DRG 1 -1.790 -14.630 -18.250 1.00 20.00
> C
> HETATM 13 C9 DRG 1 -2.550 -14.020 -19.430 1.00 20.00
> C
> HETATM 14 C10 DRG 1 -2.130 -12.760 -19.920 1.00 20.00
> C
> HETATM 15 C11 DRG 1 -2.830 -12.170 -21.000 1.00 20.00
> C
> HETATM 16 C12 DRG 1 -3.940 -12.850 -21.560 1.00 20.00
> C
> HETATM 17 C13 DRG 1 -4.350 -14.110 -21.070 1.00 20.00
> C
> HETATM 18 C14 DRG 1 -3.650 -14.700 -20.000 1.00 20.00
> C
> HETATM 19 C15 DRG 1 -3.120 -13.200 -16.630 1.00 20.00
> C
> HETATM 20 O2 DRG 1 -2.380 -12.320 -16.180 1.00 20.00
> O
> HETATM 21 N4 DRG 1 -4.400 -13.040 -16.920 1.00 20.00
> N
> HETATM 22 C16 DRG 1 -5.140 -11.770 -16.770 1.00 20.00
> C
> HETATM 23 C17 DRG 1 -6.480 -12.070 -16.090 1.00 20.00
> C
> HETATM 24 C18 DRG 1 -7.280 -10.810 -15.740 1.00 20.00
> C
> HETATM 25 C19 DRG 1 -7.030 -10.140 -14.520 1.00 20.00
> C
> HETATM 26 C20 DRG 1 -7.770 -8.980 -14.190 1.00 20.00
> C
> HETATM 27 C21 DRG 1 -8.750 -8.510 -15.090 1.00 20.00
> C
> HETATM 28 C22 DRG 1 -9.010 -9.180 -16.310 1.00 20.00
> C
> HETATM 29 C23 DRG 1 -8.270 -10.340 -16.630 1.00 20.00
> C
> HETATM 30 C24 DRG 1 -5.330 -11.100 -18.140 1.00 20.00
> C
> HETATM 31 O3 DRG 1 -6.110 -11.620 -18.940 1.00 20.00
> O
> HETATM 32 N5 DRG 1 -4.650 -9.990 -18.500 1.00 20.00
> N
> HETATM 33 C28 DRG 1 -5.010 -9.160 -19.670 1.00 20.00
> C
> HETATM 34 C27 DRG 1 -4.360 -7.820 -19.340 1.00 20.00
> C
> HETATM 35 C26 DRG 1 -3.020 -8.360 -18.860 1.00 20.00
> C
> HETATM 36 C25 DRG 1 -3.450 -9.420 -17.830 1.00 20.00
> C
> HETATM 37 C29 DRG 1 -3.750 -8.750 -16.470 1.00 20.00
> C
> HETATM 38 O4 DRG 1 -4.890 -8.380 -16.220 1.00 20.00
> O
> HETATM 39 N6 DRG 1 -2.780 -8.580 -15.540 1.00 20.00
> N
> HETATM 40 C33 DRG 1 -1.340 -8.870 -15.730 1.00 20.00
> C
> HETATM 41 C32 DRG 1 -0.700 -8.620 -14.360 1.00 20.00
> C
> HETATM 42 C31 DRG 1 -1.610 -7.510 -13.820 1.00 20.00
> C
> HETATM 43 C30 DRG 1 -3.010 -8.000 -14.200 1.00 20.00
> C
> HETATM 44 C34 DRG 1 -3.630 -9.020 -13.210 1.00 20.00
> C
> HETATM 45 O5 DRG 1 -4.710 -8.760 -12.690 1.00 20.00
> O
> HETATM 46 N7 DRG 1 -2.940 -10.140 -12.960 1.00 20.00
> N
> HETATM 47 C35 DRG 1 -3.410 -11.260 -12.130 1.00 20.00
> C
> HETATM 48 C39 DRG 1 -2.170 -12.000 -11.620 1.00 20.00
> C
> HETATM 49 O7 DRG 1 -2.260 -12.620 -10.540 1.00 20.00
> O
> HETATM 50 O8 DRG 1 -1.130 -11.970 -12.320 1.00 20.00
> O
> HETATM 51 C36 DRG 1 -4.200 -12.210 -13.040 1.00 20.00
> C
> HETATM 52 C37 DRG 1 -4.970 -13.320 -12.310 1.00 20.00
> C
> HETATM 53 C38 DRG 1 -6.220 -12.800 -11.590 1.00 20.00
> C
> HETATM 54 O6 DRG 1 -7.330 -12.870 -12.080 1.00 20.00
> O
> HETATM 55 N8 DRG 1 -6.040 -12.280 -10.390 1.00 20.00
> N
> END
>
> If you have any suggestion - I would be extremely grateful!! You have
> already been very helpful.
>
> Thanks again,
> Regina
>
> On Friday, May 30, 2003, at 01:04 PM, Daan van Aalten wrote:
>
> >
> > Hi Regina
> >
> > I really don;t understand what the problem is. If you follow eactly the
> > PDF file on GROMACS-ligand simulations from the PRODRG FAQ these
> > problems
> > don;t exist. be sure to take the PRODRG output PDB file **NOT** the
> > PDB file you put in, when you set up your system with pdb2gmx
> >
> > No need whatsoever at any stage to do editing by hand
> >
> > Daan
> >
> > On Fri, 30 May 2003, Regina R. Monaco, Ph.D. wrote:
> >
> >> You are correct - the problem lies with the "UNK" residues. I
> >> hand-edited the residue names and GROMACS atom types into the .pdb
> >> obtained from PRODRG2 and pdb2gmx ran ok.
> >>
> >> I am starting this calculation with a .mol file, which does not have
> >> any residue information - just coordinates. I am not really fond of
> >> the
> >> idea of hand-editing these peptide files as a working solution, so
> >> does
> >> anyone know of a way I can take a .mol file and have some GROMACS or
> >> some other software recognize, or allow me to graphically edit, the
> >> residues and atom types?
> >>
> >> Thanks,
> >> Regina
> >>
> >>
> >> 8. Re: Fwd: [gmx-users] D-form amino acids (Christoph
> >> Freudenberger)
> >>
> >> Message: 8
> >> Date: Fri, 30 May 2003 07:54:41 +0200
> >> From: Christoph Freudenberger
> >> <christoph.freudenberger at chemie.uni-ulm.de>
> >> Organization: University of Ulm
> >> To: gmx-users at gromacs.org
> >> Subject: Re: Fwd: [gmx-users] D-form amino acids
> >> Reply-To: gmx-users at gromacs.org
> >>
> >> Regina R. Monaco, Ph.D. wrote:
> >>> Hi Daan-
> >>>
> >>> Well, **I** am not worried, but GROMACS won't accept the
> >>> calculation. I am assuming the reason is that the program is not
> >>> certain what the atom types are, what charges to use, and how to
> >>> index
> >>> the molecule. At least, thats what the error messages indicate :>
> >>>
> >>
> >> Sound more like somethings wrong with the topology rather then
> >> the 'UNK' residues.
> >> Please post the error message and a few lines of the coordinate file.
> >>
> >> regards
> >> --
> >> Christoph Freudenberger
> >> Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785
> >>
> >> _______________________________________________
> >> gmx-users mailing list
> >> gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-request at gromacs.org.
> >>
> >
> >
> > #######################################################################
> > #######
> >
> > Dr. Daan van Aalten Wellcome Trust CDA Fellow
> > Wellcome Trust Biocentre, Dow Street TEL: ++ 44 1382 344979
> > Div. of Biol.Chem. & Mol.Microbiology FAX: ++ 44 1382 345764
> > School of Life Sciences E-mail:
> > dava at davapc1.bioch.dundee.ac.uk
> > Univ. of Dundee, Dundee DD1 5EH, UK WWW:
> > http://davapc1.bioch.dundee.ac.uk
> >
> > O C O C Visit the PRODRG server to
> > take
> > " | " | the stress out of your
> > topologies!
> > N--c--C--N--C--C--N--C--C--N--C--C--O
> > | " | "
> > http://davapc1.bioch.dundee.ac.uk/
> > C-C-O O C-C-C O
> > programs/prodrg/prodrg.html
> > "
> > O
> >
> >
>
##############################################################################
Dr. Daan van Aalten Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology FAX: ++ 44 1382 345764
School of Life Sciences E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK WWW: http://davapc1.bioch.dundee.ac.uk
O C O C Visit the PRODRG server to take
" | " | the stress out of your topologies!
N--c--C--N--C--C--N--C--C--N--C--C--O
| " | " http://davapc1.bioch.dundee.ac.uk/
C-C-O O C-C-C O programs/prodrg/prodrg.html
"
O
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