[gmx-users] topology

[Ruben Martinez Buey]

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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