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Hi,
<br>Thanks a lot for your reply. I am trying to correct the topology, but
it is not easy for me!
<br>The coordinates come from a co-crystal structure at 3.5 A.
<br>is it OK to minimize the ligand alone to check if its topology is OK?
<br>If I minimize the ligand+protein , SHAKE works OK!
<br>But if I try to minimize with GROMOS96, SHAKE (for all bonds) gives
the next error when I try to relax the water box:
<p>5. I N I T I A L I Z E R U N
<p> PERFORMING AN ENERGY MINIMISATION
<br> SHAKE: COORDINATE RESETTING CANNOT BE ACCOMPLISHED, DEVIATION
IS TOO LARGE
<br> RRPR = -0.008
<br> RPIJ2 = 0.075
<br> DIFF = -0.063
<br> NDIM = 3
<br> NCLCLO = 3
<br> NITER = 0
<br> NMOL = 1
<br> NC =
5
<br> IX(NC) = 9
<br> JX(NC) = 10
<br> CONSTR(NC)= 0.012
<br> NSKIP = 0
<br> NFIRST = 0
<br> I =
9
<br> J =
10
<br> I3 = 24
<br> J3 = 27
<br> XP(I3+M) XP(J3+M) XREF(I3+M) XREF(J3+M)
XREFIJ(M) XPIJ(M)
<br> 1.6636 1.6137
1.6793 1.6137 0.0657
0.0499
<br> 2.0197 2.0982
2.1829 2.0982 0.0847
-0.0785
<br> 1.7755 1.5176
1.4978 1.5176 -0.0199
0.2579
<p> RUNEM: EMERGENCY STOP!
<br>SHAKE FAILURE ON SOLUTE
<p>Thanks in advance for your atention
<br>with best wishes,
<br><br>
Ruben
<br>
<p>Virtual Daan wrote:
<blockquote TYPE=CITE>Ruben
<p>Use your common sense chemistry : are there any unusually long/short
<br>bonds, strange angles, groups that are not flat whereas they should
be?
<br>Is it a co-crystal structure (what resolution) or a computationally
docked
<br>complex? Could you send us the structures before and after minimisation?
<p>cheers
<p>Daan
<p>On Wed, 26 Mar 2003, Ruben Martinez Buey wrote:
<p>> Hi all,
<br>>
<br>> After an energy minimization of a protein-ligand, the ligand changes
its
<br>> structure. Some of this changes could be wrong, and this could be
a cause
<br>> of the molecular topology. Do you think it would be right to fix
or
<br>> restrain the positions of the most rigids parts in the ligand (a
complex of
<br>> 3 rings relatively rigid) and leave "flexible" the flexible side
chains of
<br>> the ligand? What would be the better way to do this?
<br>> Thanks in advance for your kind attention,
<br>> with best regards,
<br>> Ruben
<br>>
<br>>
<br>>
<br>> David wrote:
<br>>
<br>> > On Wed, 2002-11-13 at 03:11, Ruben Martinez Buey wrote:
<br>> > > Hi everybody,
<br>> > > How can I check if a molecular topology (for GROMOS96)
of a small
<br>> > > molecule (a ligand of a protein) is OK??
<br>> > > Are there another programs similar to PRODRG?? How can I check
if the
<br>> > > results of this program are OK??
<br>> > > Thanks in advance
<br>> > You may not like this, but especially for a small molecules
that are
<br>> > non-standard you have to check manually whether the toplogy makes
sense.
<br>> > This is your research and you have to be able to explain why you
have
<br>> > used such and such parameters.
<br>> >
<br>> > Having said that the first test is to do an energy minimization
or a
<br>> > short simulation of the molecule in water, see if maintains the
right
<br>> > structure and has hydrogen bonds etc.
<br>> >
<br>> > --
<br>> > Groeten, David.
<br>> > ________________________________________________________________________
<br>> > Dr. David van der Spoel,
Biomedical center, Dept. of Biochemistry
<br>> > Husargatan 3, Box 576,
75123 Uppsala, Sweden
<br>> > phone: 46 18 471 4205
fax: 46 18 511 755
<br>> > spoel@xray.bmc.uu.se spoel@gromacs.org
<a href="http://zorn.bmc.uu.se/~spoel">http://zorn.bmc.uu.se/~spoel</a>
<br>> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
<br>> > _______________________________________________
<br>> > gmx-users mailing list
<br>> > gmx-users@gromacs.org
<br>> > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
<br>> > Please don't post (un)subscribe requests to the list. Use the
<br>> > www interface or send it to gmx-users-request@gromacs.org.
<br>>
<br>> --
<br>> ___________________________________________
<br>>
<br>> Rubén Martínez-Buey. PhD student
<br>> Protein Function and Structure Dept. Lab. 352
<br>> Centro de Investigaciones Biológicas (CIB-CSIC)
<br>> C/ Velázquez, 144, 28006 MADRID (SPAIN)
<br>> Tlf: +34-91-561 18 00 ext. 4380
<br>> Fax: +34-91-562 75 18
<br>>
<br>>
<br>>
<p>##############################################################################
<p>Dr. Daan van Aalten
Wellcome Trust CDA Fellow
<br>Wellcome Trust Biocentre, Dow Street TEL: ++ 44 1382 344979
<br>Div. of Biol.Chem. & Mol.Microbiology FAX: ++ 44 1382 345764
<br>School of Life Sciences
E-mail: dava@davapc1.bioch.dundee.ac.uk
<br>Univ. of Dundee, Dundee DD1 5EH, UK WWW: <a href="http://davapc1.bioch.dundee.ac.uk">http://davapc1.bioch.dundee.ac.uk</a>
<p> O
C O
C Visit the PRODRG server
to take
<br> "
| "
| the stress out of your
topologies!
<br> N--c--C--N--C--C--N--C--C--N--C--C--O
<br> |
" |
" <a href="http://davapc1.bioch.dundee.ac.uk/">http://davapc1.bioch.dundee.ac.uk/</a>
<br> C-C-O
O C-C-C O
programs/prodrg/prodrg.html
<br> "
<br> O
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<br>Please don't post (un)subscribe requests to the list. Use the
<br>www interface or send it to gmx-users-request@gromacs.org.</blockquote>
<pre>--
___________________________________________
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</pre>
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