[gmx-users] topology

[Virtual Daan]

Ruben

Use your common sense chemistry : are there any unusually long/short
bonds, strange angles, groups that are not flat whereas they should be?
Is it a co-crystal structure (what resolution) or a computationally docked
complex? Could you send us the structures before and after minimisation?

cheers

Daan


On Wed, 26 Mar 2003, Ruben Martinez Buey wrote:

> Hi all,
>
> After an energy minimization of a protein-ligand, the ligand changes its
> structure. Some of this changes could be wrong, and this could be a cause
> of the molecular topology. Do you think it would be right to fix or
> restrain the positions of the most rigids parts in the ligand (a complex of
> 3 rings relatively rigid) and leave "flexible" the flexible side chains of
> the ligand? What would be the better way to do this?
> Thanks in advance for your kind attention,
> with best regards,
> Ruben
>
>
>
> David wrote:
>
> > On Wed, 2002-11-13 at 03:11, Ruben Martinez Buey wrote:
> > > Hi everybody,
> > > How can I check if  a molecular topology (for GROMOS96) of a small
> > > molecule (a ligand of a protein) is OK??
> > > Are there another programs similar to PRODRG?? How can I check if the
> > > results of this program are OK??
> > > Thanks in advance
> > You may not like this, but especially for a small  molecules that are
> > non-standard you have to check manually whether the toplogy makes sense.
> > This is your research and you have to be able to explain why you have
> > used such and such parameters.
> >
> > Having said that the first test is to do an energy minimization or a
> > short simulation of the molecule in water, see if maintains the right
> > structure and has hydrogen bonds etc.
> >
> > --
> > Groeten, David.
> > ________________________________________________________________________
> > Dr. David van der Spoel,        Biomedical center, Dept. of Biochemistry
> > Husargatan 3, Box 576,          75123 Uppsala, Sweden
> > phone:  46 18 471 4205          fax: 46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org  http://zorn.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > _______________________________________________
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>
> --
> ___________________________________________
>
> Rubén Martínez-Buey. PhD student
> Protein Function and Structure Dept. Lab. 352
> Centro de Investigaciones Biológicas (CIB-CSIC)
> C/ Velázquez, 144,  28006  MADRID (SPAIN)
> Tlf: +34-91-561 18 00 ext. 4380
> Fax: +34-91-562 75 18
>
>
>


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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!
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     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
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