[gmx-users] topology

Ruben Martinez Buey ruben at akilonia.cib.csic.es
Wed Mar 26 15:46:01 CET 2003 

Hi,
Thanks a lot for your reply. I am trying to correct the topology, but it is not
easy for me!
The coordinates come from a  co-crystal structure at 3.5 A.
is it OK to minimize the ligand alone to check if its topology is OK?
If I minimize the ligand+protein , SHAKE works OK!
But if I try to minimize with GROMOS96, SHAKE (for all bonds) gives the next
error when I try to relax the water box:

5. I N I T I A L I Z E   R U N

 PERFORMING AN ENERGY MINIMISATION
  SHAKE: COORDINATE RESETTING CANNOT BE ACCOMPLISHED, DEVIATION IS TOO  LARGE
 RRPR      =  -0.008
 RPIJ2     =   0.075
 DIFF      =  -0.063
 NDIM      =    3
 NCLCLO    =    3
 NITER     =    0
 NMOL      =    1
 NC        =    5
 IX(NC)    =    9
 JX(NC)    =   10
 CONSTR(NC)=   0.012
 NSKIP     =    0
 NFIRST    =    0
 I         =    9
 J         =   10
 I3        =   24
 J3        =   27
   XP(I3+M)   XP(J3+M) XREF(I3+M) XREF(J3+M)  XREFIJ(M)    XPIJ(M)
     1.6636     1.6137     1.6793     1.6137     0.0657     0.0499
     2.0197     2.0982     2.1829     2.0982     0.0847    -0.0785
     1.7755     1.5176     1.4978     1.5176    -0.0199     0.2579

 RUNEM: EMERGENCY STOP!
SHAKE FAILURE ON SOLUTE

Thanks in advance for your atention
with best wishes,

Ruben


Virtual Daan wrote:

> 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
> > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > _______________________________________________
> > > gmx-users mailing list
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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
> >
> >
> >
>
> ##############################################################################
>
> 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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--
___________________________________________

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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