[gmx-users] Topology from semiempiricaly optimized structure
Daan van Aalten
vdava at davapc1.bioch.dundee.ac.uk
Tue Jun 15 10:49:18 CEST 2004
Dear Semen
Ahhhh .. so you are the person submitting PDB files with all Z-coordinates
set to 0.000. If you think about it for a moment it's not too difficult to
see why programs would have difficulty detecting, for instance, what is an
sp2 or an sp3 carbon atom from coordinates which are a flat projection
structure without additional information.
If you just read the FAQ you will see you can directly enter an MDL
molfile, make 2 2D drawing with the JME editor or even with ASCII
characters - these format *do* contain other information than just
coordinates. Also if you put in a proper PDB file you can switch off EM -
so no need to worry about it "screwing" up your structure.
Perhaps if you don;t understand how things work it's better to read the
FAQ or E-mail me for help, rather than blurting out things on the GROMACS
mailing list.
cheers
Daan
On Sun, 13 Jun 2004, Semen Esilevsky wrote:
> Dear Daan van Aalten,
> The problem is that I already have the optimized
> geometry, so thre is no need to "guess" it. What I
> need is just to generate all the topology entries and
> assign the force constants to them, but the
> equilibrium values of bond length and angles have to
> remain the same as in the input structure. Imho, if
> PRODRG had such a feature is would be even more
> usefull for people.
>
> --- Daan van Aalten <vdava at davapc1.bioch.dundee.ac.uk>
> wrote:
> >
> > Hi Semen
> >
> > Would it be possible for you to send us the input
> > coordinates so we can
> > see what goes wrong? Do I correctly interpret your
> > E-mail to say that the
> > coordinates are screwed up even if you minimize on
> > the server?
> >
> > cheers
> >
> > Daan
> >
> > On Sat, 12 Jun 2004, Semen Esilevsky wrote:
> >
> > > You see, I've tried PRODRG and it does not work
> > for
> > > me. It disrupts the geometry I supply even if I
> > don't
> > > ask for energy minimization. I'm not sure if it is
> > a
> > > bug, but this server doesn't help much.
> > >
> > > --- Daan van Aalten
> > <vdava at davapc1.bioch.dundee.ac.uk>
> > > wrote:
> > > >
> > > > if you are happy with sticking with the ffgmx
> > force
> > > > field, the PRODRG
> > > > server will give you a topology for your
> > molecule,
> > > > see
> > > > http://davapc1.bioch.dundee.ac.uk/prodrg
> > > >
> > > > Daan
> > > >
> > > > On Fri, 11 Jun 2004, Semen Esilevsky wrote:
> > > >
> > > > > Hi all!
> > > > > I have a small molecule (a fluorescent probe),
> > > > which
> > > > > is optimized on the semiempirical level, so I
> > know
> > > > the
> > > > > geometry. As far as I understand the only way
> > to
> > > > make
> > > > > a topology for it is to write it by hands
> > using
> > > > > appropriate atom types and forcefield
> > parameters.
> > > > > However it seems to be a week of work for ~80
> > > > atoms.
> > > > > Does the program (or script) exists for this
> > > > routine
> > > > > task?
> > > > >
> > > > > Thank you in advance,
> > > > > Semen
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
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> >
> ##############################################################################
> > > > Dr. Daan van Aalten Wellcome
> > > > Trust Senior Fellow / Reader
> > > > Wellcome Trust Biocentre, Dow Street TEL: ++
> > 44
> > > > 1382 344979
> > > > Div. of Biol.Chem. & Mol.Microbiology FAX: ++
> > 44
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> > see
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> ##############################################################################
> > Dr. Daan van Aalten Wellcome
> > Trust Senior Fellow / Reader
> > 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: see
> > WWW page
> > Univ. of Dundee, Dundee DD1 5EH, UK WWW:
> > http://davapc1.bioch.dundee.ac.uk
> >
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##############################################################################
Dr. Daan van Aalten Wellcome Trust Senior Fellow / Reader
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: see WWW page
Univ. of Dundee, Dundee DD1 5EH, UK WWW: http://davapc1.bioch.dundee.ac.uk
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